Gene loci information

Transcript annotation

  • This transcript has been annotated as RanBP-type and C3HC4-type zinc finger-containing protein 1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g5087 g5087.t1 TTS g5087.t1 6819027 6819027
chr_2 g5087 g5087.t1 isoform g5087.t1 6819122 6827472
chr_2 g5087 g5087.t1 exon g5087.t1.exon1 6819122 6819301
chr_2 g5087 g5087.t1 cds g5087.t1.CDS1 6819122 6819301
chr_2 g5087 g5087.t1 exon g5087.t1.exon2 6819360 6819500
chr_2 g5087 g5087.t1 cds g5087.t1.CDS2 6819360 6819500
chr_2 g5087 g5087.t1 exon g5087.t1.exon3 6819556 6820867
chr_2 g5087 g5087.t1 cds g5087.t1.CDS3 6819556 6820867
chr_2 g5087 g5087.t1 exon g5087.t1.exon4 6820925 6823785
chr_2 g5087 g5087.t1 cds g5087.t1.CDS4 6820925 6823785
chr_2 g5087 g5087.t1 exon g5087.t1.exon5 6823864 6824499
chr_2 g5087 g5087.t1 cds g5087.t1.CDS5 6823864 6824499
chr_2 g5087 g5087.t1 exon g5087.t1.exon6 6827470 6827472
chr_2 g5087 g5087.t1 cds g5087.t1.CDS6 6827470 6827472
chr_2 g5087 g5087.t1 TSS g5087.t1 6827599 6827599

Sequences

>g5087.t1 Gene=g5087 Length=5133
ATGAATTTCGCTACCGCTGATCGTCCACGATGCATGTTACGCGATGATTTTTATCCCAGA
CAGCGTCAATTGCCACAACAGCAACGGAAATATCGAAAATTTGATTATTACAGAGAGAAT
AATGATGAATTTGACGATGACAGCACATGGTATTGGAATATGAACCAAAATCAATCAATC
AATTGTAATGGATCGTCTTCAGTAAATGCTAGAGGATCATATTACAACAATAACAATAAA
TATTATAATAAGCCTTCAGCTAGAAATGTTTCATCTGCATCTTCTGAACGCTCATCGACT
TCTGGTTTTCAGTCTTTTTTTCGCTGGTTCAAACGTGACGATAAATCTCATAGAAATTCA
AAAGACATTCGCTATCCACGCGATTTAACAAGCTCAACAGATACACTTGAGTTTGAATAT
GAAAGACGTGCACCACCACCAGTTCAGTATCGTAAAAAAGTGAAGGGAGGATATCATAAA
AATGAACCAACTGTGATCACACCACCTCAACAACCATCAAATTCTCACTTTAGCTATACA
TTTTCACAAAGTTCAAGTTGTGATAGTGTTTTTAGTACGGCTTCTTCTTTTGCTTTTGTA
CCACCAATTAAATATTTACTCAACAGAAACCATAAGCAAATTGACAGACAAATTTTGGAT
AATTCGTATACAGAAAGTTATCATAAAAGAGTAAGAGCGAGAGAACATGCACGAGAAAAT
GATAGAAACAATGAAGTGACCTTGAGAAGAAAATATCATCTATATGATGAATCAGATCAT
GAAACAAACAACAACATTTCATATGAACAAAATTATAATCAAAGAAATAATTTGAGATAT
CAAGATTTAAGTTTGCCAAATACAAAAAGATATTCACAAGAATCAAATAATCTTCCTGAT
AGTGCGAAACTAGAAGATCTCAATGTTGCATCAAAGCATAGAAGAACAAGTAGTGATTCA
TCAAAAGATAAAAGAGCTGGTGCATTTGTACATGTGAAACATAAAAGAAAAGCTCCACCG
CCTCCTCCTCTTGATTTATCACATAAATCAAAAAGTTTAACACCAAAATCGACAGGTAGA
AAAAAACGACAAGCACCATTGCCTCCAATTTCACCAACTACAAAAGTCTTGGAAGAAACT
ACATCAGCTACAAGTTTACTTGGTGATCGAGAAATTAGAGCGATAATTGAAGGAAATTTA
GAAAGAAATTCTGAAACAATTTCTGCTTCTACACCTGCTGTTCCTATGATTGAAACAGCA
AAAGAATCACCAAAAATGGAACAAAGAAAGTATGTGTCGCCATATCTTAAAATTAGAGAA
GATAGAAAATTGACAGATGAACAAAAGAGAATTTTGTTAGAACAAGTGTCTAAAAGTCAT
CAAAAGAATGATGAAACTGTAAATAATAATCATCAAATAATAAGCAATACTCAAAATCAA
GCATCAACAAGTACATTATCGATTGAAGAAGGACAACTTGTTTATCATTCTGCTGATAGT
CCAAAAATCACAAAGGATGATAAAGAAAAAGTTTTTGCTCCTTCATCGCCGATTTCACCA
AGACCTTGGTATAAAAGATCGAGCACAAACACAAATCACAATAAAGAAACAATTCCATTT
AAAAAGGAAGTAATTCTTCGAACAATGGAAAAGAGAAAGAAAAAAGATGAAAAAGATTTG
CCAGAAGTTAGTTACTCAAGAAATTCTTTCTTTGAATCAGCAAGTAAATTTAATATTTTT
GCACGTTTGACTGAAGATTCAGCAAAGAAGAAGGAAAAAGAAGCTGAAAAAAGAAGATCA
CAAATTGGAATTCCAAATATTAGTGAACTTGATCGTGAAGCAGCTGAAATTATACAGCGT
GAACATGAAGCATCAAGAGCTGCAGCATCTCTTACTAAAAATAATGACATCCCACACATT
GACGATGATGATAATGAAATTGAAGAAAGCGGAAAAAGTGCACAAGAATTGATAAGTAAA
TTTGAAGCAAATTCAGCAAATATTAATCGAATTACAGTAAATTCTAGTTTTTTACCAAGA
GAGGATTTATTTGGAAAGAAAATTTCTCAAAATGAACAGAAAGTGAGGAAGTCATTAGAA
TCACCTGACAGAAAGAAAGTTGAAAATTCTCCGCCAAAATCAAAACTTCCAGTGTCAATT
AATGGAACAAAAAAGACAAATGGATTGATGGGATTATGGACCTGTCCGTATTGCACACTT
GAAAATCCTAATTGGAAAATTATATGTGAAGCATGCGAGAAAATTAAACCATATGAGAAA
CGATGGAATGCAAATAATGAGAAGCAAGCTTCAACTCCTCCACTTCCAAGAAAATTTTCT
TATGACAATGGAAAAATTGAAAATCAATGGGATAAGAAGACAGAACTTGTTATGAAATAT
TTTCAACCAACTCAAAATAAGTCTAATGAACTTTCAAAATCTGCATCTGAAACTTTTATT
AGTAATTCATTTTTGAAAAAGTCGCCATCACCTACTCGTCGCTATCTCGGTTCACCAAAA
CTTTTGCCTCGAAAAATGTCACTTGAAAAGCAAGAAACAAAAATTGAAATGATTGCAGAA
GAATCTAATGAAAATGATAACAAATCAAGTGATGAAAATAAAATTATTGTTAAAACTATT
AAAGAAAATGATCAAAAAAGCAATGAAAATGAACCCGATTTGAATGAAATTCGATCAGCA
AGATTAGCAAGATTTAATACTTCTCTTGATATGAAGAAAAATCTTACAGAAGTTGAAAGA
TCGAATGTCACTGCTAATCGAAAACAAAGTCCAGAAAAGAAAATTACTGAAAAATTGGAT
TTTACAGATCCGATTGCATTAGAACGAGAAAAAGAAAGATTGAGAGAGAAGATTCGTGCT
ATGAATGCTAAAGCTTTGGCTGAAAAATATCCTGTACTTAAAAAGGAAGAAAATCCATCA
AATGAAATTTCAGAAGAATCGAAAATTGCACCAACTGCACCACCACTTTCACCATCAAAC
ATAACAAATACAAAACTTGGTGCAATCAAAAAAGTCTTGAAGAAACCCATCGAAACACAG
CAACAACAAAATGAAATTGAAGAACAAGCGACAGCTCTTGAAGAGAAAATAATTAATAAA
GAAATCAAAGTCCAAGAGCAACCAAAACGTGAGAAAATTTCAACAACTGTGCAGACATCT
GTAGATATTAAATTGAGAAAAAAATCAGAAGATCTTGTGCCCACAACTGTCGTTGAGCTC
GTAAAAAAGAATAATAATGAAGAAAAAATTAAGAAAGAAGATGATGAAATACCACAAGTG
ACTTTTAGATTCCCACTCAATACAAATACAATAGCCATTAATAAAATTTTAAGAAATTTG
GAAAATGCAATTGCTGATGGAAAGCATTTAGAAGCTGCTGAATTTGCAAAAGATTTAGCT
AAACTTAAAGTTCCATTATCAGTTACAAGGCAAAAAGACCGACCGAAATCAGAAGTAGAA
ATTGAAGTTTCAAAAGTCAAAGCATGGTTGAGCATAAAAGAAAACTTTCGAGAGATGGAA
GTAAATTGTTATGAAATTTCATCAAATATGACAATTGATGATTTGAAAAAGCAAATTTCC
AAAGATTATTATATACCAATAGAAAAGCAGAAAATTACAATTAATGGATTATCATGTGAT
GGTAGAAAGTCATTAAAGGAAATACCAACAAAAATTGAAAATGGTATAAGAATTAATGTA
TCAGTTGGCACAAGTAATGATGAACAGCAAATTGCTTCAAAAAAAGATGAATCAGAATCA
GATGATGAGATACAAAATGAAAAGGTTGGCAGCTTTGATGTAGCAGTGGGAGGTGCAAAC
AAAAATAAGCAAAAGATTGAAGATAATGGTTGGGAATGTCCACTTTGCACTTTGATAAAT
TTACCAAGCAGACAACAATGTTTAGCATGCTCAACATCAAAACCTCTCCCTAATAAAATG
ACAAAGCTCAAAGAACTTGAATATCATTTTAAAGTTAGTGAAGATTTAAAAACATTTTTT
GAAATGGACAAAGTTGATTTGCGACCAAAAAATTTAGAGAAAAATGATCTCAATCGAAAG
AGTGCTCATAGAAAGAGTTCAGATCTTTTAAATATTTTGGAAGATGATAAAAATTTGCAA
AAGAAAGAAATTTTGCCTCAACAAAATACAATAGTCATGACTGCATCGATTGCTAGTCCA
AATATCACAAAAAACAAGTATCGTGGTGTTGATAATTTTAGTCCATATAAATCTTATATT
TTTCCAAAAGTGACAACATCAAATAATAATGAAATTAGCAAACCGATAATTACAAACGTT
ATATATAAATCTAGTCAAAGTGTTACCAAAGAGCCTCTGTTATCGATTAATGCTCAAAAA
AGTCATTATCAAGAATTAATGAACTTGGAAGTATCAGATGTTGTCCCAAATACAAGTAAA
TTTGAATGCTCGATATGTTTTATGGAAATTGAGTCAAAACAAGGAGTATGCTTACGAGAT
TGTTTACATTCATTTTGCAAAATTTGTCTTCAAAGTCATATTAAGTATAGTGAGGAGGCT
GAAATAAAATGTCCATATATTGATGACACTTACAGCTGTCAAAGTTTCCTGCAAGAAAGA
GAAGTTAGAGGTTTAGTTTCAAAGGATGATTACGAAAAGCATTTATCGCGCTCTGTAAGA
TTAGCAGAGAATAAAATTGAAAATGCATTTCATTGCAAAACTCCAAATTGCAAAGGTTGG
TGCATATTTGAGGATAATACAAATTCTTTCAAATGCCCCGTATGTACTATTTTGAATTGC
ATAACTTGTGGGGCAATTCATGATGGACTGAATTGTAAGCAGTATCAAGATCATTTAAGC
AAAGGATCTGATGAGGAGTCAGTAAATCAAACAAAAAAATTATTGCAAGAATTGATTGAT
AAAGATGAAGCTATGAATTGCCCTACATGTCATATATTTTTATTAAAAAAGTGGGGTTGC
GATTGGCTAAGATGTTCTTTTTGTAAAACAGAGATTTGTTGGGTAACAAAGAAAAAACGA
TGGGGGCCTGAAGGAAAAGGAGATTATTCTGATGGTTGTAAATGTGGATTTAATGGAAAG
AAATGTTCTCCTAAGTGCACTTACTGTCATTAA

>g5087.t1 Gene=g5087 Length=1710
MNFATADRPRCMLRDDFYPRQRQLPQQQRKYRKFDYYRENNDEFDDDSTWYWNMNQNQSI
NCNGSSSVNARGSYYNNNNKYYNKPSARNVSSASSERSSTSGFQSFFRWFKRDDKSHRNS
KDIRYPRDLTSSTDTLEFEYERRAPPPVQYRKKVKGGYHKNEPTVITPPQQPSNSHFSYT
FSQSSSCDSVFSTASSFAFVPPIKYLLNRNHKQIDRQILDNSYTESYHKRVRAREHAREN
DRNNEVTLRRKYHLYDESDHETNNNISYEQNYNQRNNLRYQDLSLPNTKRYSQESNNLPD
SAKLEDLNVASKHRRTSSDSSKDKRAGAFVHVKHKRKAPPPPPLDLSHKSKSLTPKSTGR
KKRQAPLPPISPTTKVLEETTSATSLLGDREIRAIIEGNLERNSETISASTPAVPMIETA
KESPKMEQRKYVSPYLKIREDRKLTDEQKRILLEQVSKSHQKNDETVNNNHQIISNTQNQ
ASTSTLSIEEGQLVYHSADSPKITKDDKEKVFAPSSPISPRPWYKRSSTNTNHNKETIPF
KKEVILRTMEKRKKKDEKDLPEVSYSRNSFFESASKFNIFARLTEDSAKKKEKEAEKRRS
QIGIPNISELDREAAEIIQREHEASRAAASLTKNNDIPHIDDDDNEIEESGKSAQELISK
FEANSANINRITVNSSFLPREDLFGKKISQNEQKVRKSLESPDRKKVENSPPKSKLPVSI
NGTKKTNGLMGLWTCPYCTLENPNWKIICEACEKIKPYEKRWNANNEKQASTPPLPRKFS
YDNGKIENQWDKKTELVMKYFQPTQNKSNELSKSASETFISNSFLKKSPSPTRRYLGSPK
LLPRKMSLEKQETKIEMIAEESNENDNKSSDENKIIVKTIKENDQKSNENEPDLNEIRSA
RLARFNTSLDMKKNLTEVERSNVTANRKQSPEKKITEKLDFTDPIALEREKERLREKIRA
MNAKALAEKYPVLKKEENPSNEISEESKIAPTAPPLSPSNITNTKLGAIKKVLKKPIETQ
QQQNEIEEQATALEEKIINKEIKVQEQPKREKISTTVQTSVDIKLRKKSEDLVPTTVVEL
VKKNNNEEKIKKEDDEIPQVTFRFPLNTNTIAINKILRNLENAIADGKHLEAAEFAKDLA
KLKVPLSVTRQKDRPKSEVEIEVSKVKAWLSIKENFREMEVNCYEISSNMTIDDLKKQIS
KDYYIPIEKQKITINGLSCDGRKSLKEIPTKIENGIRINVSVGTSNDEQQIASKKDESES
DDEIQNEKVGSFDVAVGGANKNKQKIEDNGWECPLCTLINLPSRQQCLACSTSKPLPNKM
TKLKELEYHFKVSEDLKTFFEMDKVDLRPKNLEKNDLNRKSAHRKSSDLLNILEDDKNLQ
KKEILPQQNTIVMTASIASPNITKNKYRGVDNFSPYKSYIFPKVTTSNNNEISKPIITNV
IYKSSQSVTKEPLLSINAQKSHYQELMNLEVSDVVPNTSKFECSICFMEIESKQGVCLRD
CLHSFCKICLQSHIKYSEEAEIKCPYIDDTYSCQSFLQEREVRGLVSKDDYEKHLSRSVR
LAENKIENAFHCKTPNCKGWCIFEDNTNSFKCPVCTILNCITCGAIHDGLNCKQYQDHLS
KGSDEESVNQTKKLLQELIDKDEAMNCPTCHIFLLKKWGCDWLRCSFCKTEICWVTKKKR
WGPEGKGDYSDGCKCGFNGKKCSPKCTYCH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g5087.t1 CDD cd17039 Ubl_ubiquitin_like 1184 1240 4.0011E-6
16 g5087.t1 CDD cd16633 mRING-HC-C3HC3D_RBR_HOIL1 1481 1533 9.85453E-28
14 g5087.t1 Coils Coil Coil 1023 1043 -
11 g5087.t1 Gene3D G3DSA:3.10.20.90 - 1165 1235 3.7E-5
13 g5087.t1 Gene3D G3DSA:2.20.28.140 - 1285 1336 7.5E-10
12 g5087.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 1477 1566 5.6E-12
22 g5087.t1 MobiDBLite mobidb-lite consensus disorder prediction 230 249 -
28 g5087.t1 MobiDBLite mobidb-lite consensus disorder prediction 292 371 -
26 g5087.t1 MobiDBLite mobidb-lite consensus disorder prediction 306 327 -
23 g5087.t1 MobiDBLite mobidb-lite consensus disorder prediction 688 711 -
25 g5087.t1 MobiDBLite mobidb-lite consensus disorder prediction 688 716 -
24 g5087.t1 MobiDBLite mobidb-lite consensus disorder prediction 1247 1267 -
27 g5087.t1 MobiDBLite mobidb-lite consensus disorder prediction 1250 1267 -
2 g5087.t1 PANTHER PTHR22770:SF35 RANBP-TYPE AND C3HC4-TYPE ZINC FINGER-CONTAINING PROTEIN 1 1114 1317 4.7E-107
4 g5087.t1 PANTHER PTHR22770 UBIQUITIN CONJUGATING ENZYME 7 INTERACTING PROTEIN-RELATED 1114 1317 4.7E-107
3 g5087.t1 PANTHER PTHR22770:SF35 RANBP-TYPE AND C3HC4-TYPE ZINC FINGER-CONTAINING PROTEIN 1 1418 1710 4.7E-107
5 g5087.t1 PANTHER PTHR22770 UBIQUITIN CONJUGATING ENZYME 7 INTERACTING PROTEIN-RELATED 1418 1710 4.7E-107
1 g5087.t1 Pfam PF00641 Zn-finger in Ran binding protein and others 1291 1315 5.2E-6
20 g5087.t1 ProSitePatterns PS01358 Zinc finger RanBP2-type signature. 733 752 -
19 g5087.t1 ProSitePatterns PS01358 Zinc finger RanBP2-type signature. 1291 1310 -
21 g5087.t1 ProSitePatterns PS00518 Zinc finger RING-type signature. 1501 1510 -
31 g5087.t1 ProSiteProfiles PS50199 Zinc finger RanBP2 type profile. 729 758 8.163
29 g5087.t1 ProSiteProfiles PS50053 Ubiquitin domain profile. 1159 1227 9.09
32 g5087.t1 ProSiteProfiles PS50199 Zinc finger RanBP2 type profile. 1287 1316 9.54
33 g5087.t1 ProSiteProfiles PS51873 TRIAD supradomain profile. 1479 1699 28.032
30 g5087.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 1483 1525 10.38
17 g5087.t1 SMART SM00547 zf_4 731 755 0.0072
18 g5087.t1 SMART SM00547 zf_4 1289 1313 8.1E-5
10 g5087.t1 SUPERFAMILY SSF54236 Ubiquitin-like 1180 1242 8.98E-7
6 g5087.t1 SUPERFAMILY SSF90209 Ran binding protein zinc finger-like 1288 1314 3.66E-5
9 g5087.t1 SUPERFAMILY SSF57850 RING/U-box 1478 1560 2.78E-10
7 g5087.t1 SUPERFAMILY SSF57850 RING/U-box 1553 1618 1.66E-9
8 g5087.t1 SUPERFAMILY SSF57850 RING/U-box 1633 1686 5.3E-7

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5087/g5087.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5087.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values