Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000006

Orthogroup ID

OG0004276

Physical Location & Seq

Genomic Coordinates Reverse (-)

47848507 .. 47851353

Gene Structure 2847 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_6G00427230.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 747 bp

ATGGGGCCTAGGTGGAAAGGAAAGGGCTTCAAAGCTAAAGCTCTTTCAGACCCCATGTCAAAGATAGTACTGCAGCTTCAATCTTCTCTAAATCAATCAAATTGTGAAGGGTTGCTATGTGGGTGTAGTGTGCTTCTCTCAGTGGAAGCAGAACAAGCTGATCTCCTCAATCGTTCGTGCTTTGGTGAAGCCATGGTTACAGCTGAGAAGGATAAGCAATGGTTTGAGTTGAGTTTGGAGGAGGGCTTTTATCTGAGCTATGCTCTAAAATGCCTCAGGATAGTTGAAGATAAATGTCCGAAGAGCGATGAGCAGCTATGGCAGTGCATGAAGTCTAAAAGTGCATTGTTTCCGTATTTTTATAAGGCGTATTCTCATCTTAGGATGAAGAATTGGGTTGTTATGTCGGGGATTACATATGGTGCAGACTTTGTTGCTTACCGTCATCATCCGGAGTTGGTACATTCTGAATATGCAGTGATTGTGTCCTTGGAGGAGGAGGAGGGTGGTGCAAATAATCGATTGAGGGTGTGGTCTGATGTGCATTGCGCTACTCGGCTTTGTGGAGGTGTGGCAAAGACATTACTGGTTCTTGATATCAGCAGAAATGGTCATAGTGCAGACTCTCCATCGTGTTTGGAGAGTTATACTGTCAAGGAGCGCACGATCACAAGATGGAATCCAGAACAGTGCCGCGAAGATCATACAATGGTTGAAAGTGAAAATGGAGCCAAGGAAGAGATTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000213 GO:0000214 GO:0000278 GO:0000281 GO:0000379 GO:0000394 GO:0000910 GO:0003006 GO:0003674 GO:0003824 GO:0004518 GO:0004519 GO:0004521 GO:0004540 GO:0004549 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006388 GO:0006396 GO:0006399 GO:0006725 GO:0006807 GO:0007049 GO:0007275 GO:0008033 GO:0008150 GO:0008152 GO:0008356 GO:0008380 GO:0009790 GO:0009791 GO:0009793 GO:0009987 GO:0010069 GO:0010070 GO:0010154 GO:0010467 GO:0016070 GO:0016787 GO:0016788 GO:0016892 GO:0016894 GO:0022402 GO:0022414 GO:0032501 GO:0032502 GO:0032991 GO:0034470 GO:0034641 GO:0034660 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0051301 GO:0061458 GO:0061640 GO:0071704 GO:0090304 GO:0090305 GO:0090501 GO:0090502 GO:0140098 GO:0140101 GO:1901360 GO:1902494 GO:1902555 GO:1903047 GO:1905348

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

tRNA_int_endo tRNA_int_endo_N

Protein Analysis

248

Amino Acids

28.06

Weight (kDa)

5.85

Isoelectric Point (pI)

52.28

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
tRNA_int_endo_N	PF02778	36 - 107	9.5e-13	tRNA intron endonuclease, N-terminal domain
tRNA_int_endo	PF01974	121 - 203	1.2e-14	tRNA intron endonuclease, catalytic C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0004276)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G38890
fragaria_vesca	FvH4_6g01503 FvH4_6g01503 FvH4_6g01503 FvH4_6g01503 FvH4_6g01510
malus_domestica	MD11G1123700.v1.1 MD11G1124300.v1.1 MD12G1250600.v1.1
prunus_persica	Prupe.6G093000_v2.0.a1 Prupe.6G093000_v2.0.a1 Prupe.6G352700_v2.0.a1 Prupe.6G352700_v2.0.a1
pyrus_communis	pycom11g10450 pycom12g23060
rosa_chinensis	RchiOBHm_Chr3g0449171 RchiOBHm_Chr3g0449181 RchiOBHm_Chr5g0061031
rosa_laevigata	RLG00000035421
rosa_multiflora	Rmu_co8387241.1_g000001 Rmu_sc0000640.1_g000004 Rmu_sc0004874.1_g000009 Rmu_sc0006661.1_g000007
rosa_roxburghii	Rroxscaffold_1G00019610 Rroxscaffold_6G00427230
rosa_rugosa	Rorug02G0618600 Rorug05G0336200
rosa_samantha	Rh1AG412000 Rh3AG016900
rosa_wichuraiana	Rw3G001270 Rw3G001280 Rw5G037580

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	363
AccII	CGCG	1 cut(s)	696
AccIII	TCCGGA	1 cut(s)	451
AciI	CCGC	1 cut(s)	694
AfaI	GTAC	2 cut(s)	69, 462
AgsI	TTSAA	4 cut(s)	31, 80, 287, 716
AhdI	GACNNNNNGTC	1 cut(s)	55
AluBI	AGCT	7 cut(s)	35, 41, 76, 158, 203, 258, 316
AluI	AGCT	7 cut(s)	35, 41, 76, 158, 203, 258, 316
Aor13HI	TCCGGA	1 cut(s)	451
AoxI	GGCC	1 cut(s)	5
ApeKI	GCWGC	2 cut(s)	73, 313
AspA2I	CCTAGG	1 cut(s)	8
AspLEI	GCGC	2 cut(s)	551, 663
AspS9I	GGNCC	1 cut(s)	5
AsuHPI	GGTGA	1 cut(s)	197
AvrII	CCTAGG	1 cut(s)	8
AxyI	CCTNAGG	1 cut(s)	275
BarI	GAAGNNNNNNTAC	2 cut(s)	60, 92
BbvI	GCAGC	2 cut(s)	85, 325
BccI	CCATC	2 cut(s)	637, 669
BfaI	CTAG	1 cut(s)	9
BfmI	CTRYAG	1 cut(s)	71
BisI	GCNGC	3 cut(s)	74, 314, 694
BlnI	CCTAGG	1 cut(s)	8
BlsI	GCNGC	3 cut(s)	75, 315, 695
BmcAI	AGTACT	1 cut(s)	69
BmeRI	GACNNNNNGTC	1 cut(s)	55
BmgT120I	GGNCC	1 cut(s)	5
BmiI	GGNNCC	2 cut(s)	6, 730
BplI	GAGNNNNNCTC	2 cut(s)	247, 279
Bsa29I	ATCGAT	1 cut(s)	520
BsaJI	CCNNGG	4 cut(s)	8, 192, 489, 732
BsaWI	WCCGGW	1 cut(s)	451
Bse1I	ACTGG	1 cut(s)	591
Bse21I	CCTNAGG	1 cut(s)	275
Bse3DI	GCAATG	2 cut(s)	224, 544
BseAI	TCCGGA	1 cut(s)	451
BseCI	ATCGAT	1 cut(s)	520
BseDI	CCNNGG	4 cut(s)	8, 192, 489, 732
BseGI	GGATG	2 cut(s)	390, 448
BseMI	GCAATG	2 cut(s)	224, 544
BseMII	CTCAG	4 cut(s)	153, 195, 245, 289
BseNI	ACTGG	1 cut(s)	591
BseRI	GAGGAG	5 cut(s)	155, 254, 509, 512, 515
BseXI	GCAGC	2 cut(s)	85, 325
BsgI	GTGCAG	2 cut(s)	444, 639
Bsh1236I	CGCG	1 cut(s)	696
BshFI	GGCC	1 cut(s)	7
BshVI	ATCGAT	1 cut(s)	520
BsiSI	CCGG	1 cut(s)	452
BsnI	GGCC	1 cut(s)	7
Bsp13I	TCCGGA	1 cut(s)	451
Bsp143I	GATC	3 cut(s)	160, 666, 700
Bsp19I	CCATGG	1 cut(s)	192
BspACI	CCGC	1 cut(s)	694
BspANI	GGCC	1 cut(s)	7
BspCNI	CTCAG	4 cut(s)	152, 196, 246, 288
BspDI	ATCGAT	1 cut(s)	520
BspEI	TCCGGA	1 cut(s)	451
BspFNI	CGCG	1 cut(s)	696
BspLI	GGNNCC	2 cut(s)	6, 730
BspMAI	CTGCAG	1 cut(s)	75
BspQI	GCTCTTC	1 cut(s)	296
BsrDI	GCAATG	2 cut(s)	224, 544
BsrI	ACTGG	1 cut(s)	591
BssECI	CCNNGG	4 cut(s)	8, 192, 489, 732
BssMI	GATC	3 cut(s)	160, 666, 700
BssT1I	CCWWGG	4 cut(s)	8, 192, 489, 732
Bst4CI	ACNGT	3 cut(s)	443, 652, 690
Bst6I	CTCTTC	2 cut(s)	296, 732
BstDEI	CTNAG	5 cut(s)	139, 204, 254, 275, 380
BstDSI	CCRYGG	1 cut(s)	192
BstF5I	GGATG	2 cut(s)	390, 448
BstFNI	CGCG	1 cut(s)	696
BstHHI	GCGC	2 cut(s)	551, 663
BstKTI	GATC	3 cut(s)	163, 669, 703
BstMBI	GATC	3 cut(s)	160, 666, 700
BstMWI	GCNNNNNNNGC	2 cut(s)	155, 319
BstSFI	CTRYAG	1 cut(s)	71
BstUI	CGCG	1 cut(s)	696
BstV1I	GCAGC	2 cut(s)	85, 325
Bsu15I	ATCGAT	1 cut(s)	520
Bsu36I	CCTNAGG	1 cut(s)	275
BsuRI	GGCC	1 cut(s)	7
BsuTUI	ATCGAT	1 cut(s)	520
BtgI	CCRYGG	1 cut(s)	192
BtgZI	GCGATG	1 cut(s)	321
BtsCI	GGATG	2 cut(s)	390, 448
BtsI	GCAGTG	2 cut(s)	329, 483
BtsIMutI	CAGTG	4 cut(s)	147, 329, 483, 695
CfoI	GCGC	2 cut(s)	551, 663
Cfr13I	GGNCC	1 cut(s)	5
ClaI	ATCGAT	1 cut(s)	520
Csp6I	GTAC	2 cut(s)	68, 461
CviAII	CATG	3 cut(s)	55, 193, 328
CviQI	GTAC	2 cut(s)	68, 461
DdeI	CTNAG	5 cut(s)	139, 204, 254, 275, 380
DpnI	GATC	3 cut(s)	162, 668, 702
DpnII	GATC	3 cut(s)	160, 666, 700
DriI	GACNNNNNGTC	1 cut(s)	55
Eam1104I	CTCTTC	2 cut(s)	296, 732
Eam1105I	GACNNNNNGTC	1 cut(s)	55
EarI	CTCTTC	2 cut(s)	296, 732
Eco130I	CCWWGG	4 cut(s)	8, 192, 489, 732
Eco32I	GATATC	1 cut(s)	598
Eco81I	CCTNAGG	1 cut(s)	275
EcoO109I	RGGNCCY	1 cut(s)	5
EcoRV	GATATC	1 cut(s)	598
EcoT14I	CCWWGG	4 cut(s)	8, 192, 489, 732
ErhI	CCWWGG	4 cut(s)	8, 192, 489, 732
FaeI	CATG	3 cut(s)	58, 196, 331
FatI	CATG	3 cut(s)	54, 192, 327
FauNDI	CATATG	1 cut(s)	418
Fnu4HI	GCNGC	3 cut(s)	74, 314, 694
FokI	GGATG	2 cut(s)	397, 435
Fsp4HI	GCNGC	3 cut(s)	74, 314, 694
FspBI	CTAG	1 cut(s)	9
GlaI	GCGC	2 cut(s)	550, 662
GluI	GCNGC	3 cut(s)	74, 314, 694
HaeIII	GGCC	1 cut(s)	7
HapII	CCGG	1 cut(s)	452
HhaI	GCGC	2 cut(s)	551, 663
Hin1II	CATG	3 cut(s)	58, 196, 331
Hin6I	GCGC	2 cut(s)	549, 661
HinP1I	GCGC	2 cut(s)	549, 661
HinfI	GANTC	2 cut(s)	623, 679
HpaII	CCGG	1 cut(s)	452
HphI	GGTGA	1 cut(s)	197
Hpy188I	TCNGA	5 cut(s)	49, 255, 300, 469, 538
Hpy188III	TCNNGA	4 cut(s)	277, 452, 593, 683
HpyAV	CCTTC	2 cut(s)	101, 202
HpyCH4III	ACNGT	3 cut(s)	443, 652, 690
HpyCH4V	TGCA	8 cut(s)	73, 327, 344, 425, 476, 512, 544, 620
HpyF10VI	GCNNNNNNNGC	2 cut(s)	155, 319
HpyF3I	CTNAG	5 cut(s)	139, 204, 254, 275, 380
Hsp92II	CATG	3 cut(s)	58, 196, 331
HspAI	GCGC	2 cut(s)	549, 661
Kpn2I	TCCGGA	1 cut(s)	451
Kzo9I	GATC	3 cut(s)	160, 666, 700
LguI	GCTCTTC	1 cut(s)	296
LmnI	GCTCC	2 cut(s)	658, 728
LpnPI	CCDG	4 cut(s)	262, 465, 572, 696
Lsp1109I	GCAGC	2 cut(s)	85, 325
MaeI	CTAG	1 cut(s)	9
MaeIII	GTNAC	1 cut(s)	196
MalI	GATC	3 cut(s)	162, 668, 702
MboI	GATC	3 cut(s)	160, 666, 700
MboII	GAAGA	5 cut(s)	75, 299, 313, 400, 710
MluCI	AATT	2 cut(s)	100, 391
MlyI	GAGTC	1 cut(s)	617
MroI	TCCGGA	1 cut(s)	451
MspA1I	CMGCKG	1 cut(s)	203
MspI	CCGG	1 cut(s)	452
MvnI	CGCG	1 cut(s)	696
MwoI	GCNNNNNNNGC	2 cut(s)	155, 319
NcoI	CCATGG	1 cut(s)	192
NdeI	CATATG	1 cut(s)	418
NdeII	GATC	3 cut(s)	160, 666, 700
NlaIII	CATG	3 cut(s)	58, 196, 331
NlaIV	GGNNCC	2 cut(s)	6, 730
NmeAIII	GCCGAG	1 cut(s)	535
PciSI	GCTCTTC	1 cut(s)	296
PfeI	GAWTC	1 cut(s)	679
PkrI	GCNGC	3 cut(s)	75, 315, 695
PleI	GAGTC	1 cut(s)	617
PpsI	GAGTC	1 cut(s)	617
PsiI	TTATAA	1 cut(s)	363
PspN4I	GGNNCC	2 cut(s)	6, 730
PspPI	GGNCC	1 cut(s)	5
PstI	CTGCAG	1 cut(s)	75
PvuII	CAGCTG	1 cut(s)	203
RsaI	GTAC	2 cut(s)	69, 462
RsaNI	GTAC	2 cut(s)	68, 461
SapI	GCTCTTC	1 cut(s)	296
SatI	GCNGC	3 cut(s)	74, 314, 694
Sau3AI	GATC	3 cut(s)	160, 666, 700
Sau96I	GGNCC	1 cut(s)	5
ScaI	AGTACT	1 cut(s)	69
SchI	GAGTC	1 cut(s)	617
SetI	ASST	9 cut(s)	14, 37, 43, 78, 160, 205, 260, 318, 571
SfcI	CTRYAG	1 cut(s)	71
Sse9I	AATT	2 cut(s)	100, 391
SsiI	CCGC	1 cut(s)	694
SspMI	CTAG	1 cut(s)	9
StyI	CCWWGG	4 cut(s)	8, 192, 489, 732
TaaI	ACNGT	3 cut(s)	443, 652, 690
TaqI	TCGA	1 cut(s)	520
TasI	AATT	2 cut(s)	100, 391
TatI	WGTACW	1 cut(s)	67
TauI	GCSGC	1 cut(s)	696
TfiI	GAWTC	1 cut(s)	679
TscAI	CASTG	4 cut(s)	147, 329, 483, 695
TseI	GCWGC	2 cut(s)	73, 313
TspDTI	ATGAA	2 cut(s)	344, 401
TspGWI	ACGGA	1 cut(s)	342
TspRI	CASTG	4 cut(s)	147, 329, 483, 695
XmaJI	CCTAGG	1 cut(s)	8
XspI	CTAG	1 cut(s)	9
ZrmI	AGTACT	1 cut(s)	69

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.