General information for g11887.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ras-responsive element-binding protein 1.
Parent gene
- The parent gene g11887 is located on chr_1: 18965998..18979783 (- strand)
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_1 | g11887 | g11887.t1 | TTS | g11887.t1 | 18965287 | 18965287 |
| chr_1 | g11887 | g11887.t1 | isoform | g11887.t1 | 18965998 | 18979783 |
| chr_1 | g11887 | g11887.t1 | exon | g11887.t1.exon1 | 18965998 | 18968789 |
| chr_1 | g11887 | g11887.t1 | cds | g11887.t1.CDS1 | 18965998 | 18968789 |
| chr_1 | g11887 | g11887.t1 | exon | g11887.t1.exon2 | 18968853 | 18969488 |
| chr_1 | g11887 | g11887.t1 | cds | g11887.t1.CDS2 | 18968853 | 18969488 |
| chr_1 | g11887 | g11887.t1 | exon | g11887.t1.exon3 | 18979768 | 18979783 |
| chr_1 | g11887 | g11887.t1 | cds | g11887.t1.CDS3 | 18979768 | 18979783 |
| chr_1 | g11887 | g11887.t1 | TSS | g11887.t1 | 18980433 | 18980433 |
Sequences
>g11887.t1 Gene=g11887 Length=3444
ATGGAACAAATTGATGTCGCTTACAACAACAGCAATAGTAACATTAAAATGGAACGTCGT
ACATCAACAAATTCTGAATCGTCAATAGAACAAACCGAAGTGAGTTCATCGAATAAAACA
CTAAGCACATCAGACGCAAATTCATCATTGGCACTAAAAACAAGTCAAGATAGCGATAAT
GTAGAATCAGATGAGAATGAAGACTATTTAAATAATAATACACGTAAAAGTAACAACAAA
AATGATGATGGCGGTAATGAGTCGTCGTCAGTAATGAGTCATCGAACGAACACCAAAGAT
ACAATAGTAAGACGCGACAATTTATCAAAATTAATGGATAAAATGCTTCAGAAAAAAATT
ATGAGTGTGGCAACACGTCACAACAACAACAACAATCATAGTTCAGAAGAAAATTTAAAT
GATGCTGAAAATGAAAGACAAAACGATTCAATGACCAAAGATGACACAACAAAATATGTA
TGTCCCATTTGTGAAGCAGTTTCAACTACTCAACACGACTTTACAAATCATATTCGCAAT
CACAATAACACACGCGATTCATCTGATGATAGTTCTTCATTCACATGTCGCATTTGCTCA
AAAGTTTTATCATCAGCTTCTTCTCTTGATCGTCATGTTCTCGTACATACAGGAGAAAGA
CCTTTCAATTGCAAATTCTGCAATTTAACTTTTACAACGAATGGCAATATGCATCGACAT
ATGCGAACGCACAAACAACCTCAACACGATCGTGAAAGTTACGAAAGTGATGGCTCTACA
GACTCTAGTGGTAGTTCTAATCGAAAAGTCAGCAATTATTCTAATAAAAGAAAAAGTGCC
GATGATGAACACACTAATAAACGCAAAATTCGAGCAGTAAATTACAATAATAATACAATT
ACATCGCCAAATTTTTTGCAACAACAACAAAATCAAAAATTTTGCTGCCCTGTTTGCATT
CGCAATGATTTTCCAAGTATGATTAGTCTTGAAAATCACATGGACAAAGAACATCCAACT
ATTCCAGCCAAATGTCGTCATTGTGAAATGGTTTTCAAGAGCCATAAAGCACTAAATGCA
CATCGTTGCGGTCATAATAAATCAAATAATGTGCAACAGGGCTTTGGTGATCTCTCGTCA
ATCATTGACTTTTCATGCGAAAAATTTCCACTGATTGCACAGAAAATGTGCGAACAATCA
ATCCGTACACCTATTACAAATCAAAAATATGAATGTCGCATATGCTTTAGAGCTTTTCCT
TGTGCCAGTGCTGTTGAAATTCATATGCGTGAATGTAGTGATTCCGTAACATCAAACAAA
AGACGACGTTCACGTAGTGAAACATCAGTCGATGATGAAGAAGTACGACGTGATGATTTT
TTTGCTAATCTTGCACTTCAAAATAGACCACCATCATCAACTTCATCTATTGATAAATCT
TTTTCAAATAAAACAATGGTAATTAAGCAAGAAATATGCGAAACTTCACCATACTTGCAA
TATTTTAATGAGGCACGTGATTTTGCTGATATCGAGTCAATAATTAAAGCAACATCATCT
GGTGGTTTAGAAAAACCAATTCCTGAAAAAGATCAACATCTCTATAACCGTGAAGAAGAA
GAAGCTCAAGATGCTTTCACACAAGAATTTCGTAAAATGAAATTACGTGGTGAATTTCCG
TGTCGCTTATGTACAATGGTTTTTCCAAACTTACGTGCACTTAAGGGTCACAATCGAGTG
CATTTATCAGCTTCAGGTCCAGGACCATACCGTTGTAATATGTGTACATTTTCGATAAAT
GACAAACAAGCACTCATTCGTCATATGCGCAATCATAATGGTGACCGTCCATATGAATGT
GCTCTTTGCAACTATGCTTTTACTACAAAAGCAAATTGTGAACGACATCTTAGAAATCGC
CATGGTAAATTGACACGTGAAGATGTCAAAAGAGCAATCATTTATCATCCTTCAGAAGAC
TCGAGTGTTGACGATCATAGCAAGAAAATTGCATTATATGCACAAAATAATCGCTATAAT
CGAAGCAATGATGATGAAGATGAAGAAGAAAATGACGATGAATTAGATCCAAGTGGAAGA
AGCACTCCAGTTTCACATTTGAAAGATATTTTGCAATCACGTAAAGATGATTCACCAAGT
CGTATTCAAGTAAAAAGTTTAGAAAAATTGAAATCACAACAAAATTTTGAAAATGACATT
GAAGAAGAACTCAATGAGAGTGCACAGCGTTCAGGAGTTGATTTATCAATGGATGTACTA
GATTTGAGCAAAAAAACTGATTCTTTTGCTCATAATAATGGAAATGATGCTTCTGGTGAA
GATGAAAGTGATCAAGAAAGAAACAATAATGATGATGATGATGAACTTCACCCTGAAATT
CCTAAATTTGATCTCGGAATGTTTGAAAAAAGTTTCTTAATGCAGCAACAATTATTTACT
GAAGCATTGCCAAAACTTGATCCCGCTCAAATGTTTAATTTGGCTCAAATGTATCGAACA
TTTGGCTTTCCAACACCAGGTTTTCCAATTCATCCGGCATTGTTTCTTCAAAATCCTTTA
CTTTTAAATGATACAATGAAAAATTTCTTTCAAAAAGATTTGATGCCACCAACTCCGCCT
TCATCAAATAATAATGCAACAACTAATACAGGAAGCATGTCAGGTGGAAGTATGATTGTA
AATCCATTTGTTTCACCTGATTCATCACCAACTGCTCCACCAAATCAACAGACACGCATC
GATCAATCACCTATCACAAATTCCATTCCAGTTCCACCATTTCCACCAACACCTCAAGAA
TCGCCAAAAAAAGTCTCAACGCCAAATTCTTCAAATATCAATCTCGCTAATCATTCTGGA
CCAGTTAAAATGGTCATTAAGAATGGTGTGCTCATGCCAAAACAAAAACAACGTCGTTAT
CGAACTGAACGACCATTTGCATGTGAGCATTGTAGTGCTCGTTTTACACTTAGATCAAAT
ATGGAACGACATATTAAGCAACAACATCCACAATTTTGGGCACAGAGACAACGTGGAAAT
CATGGTCTAATGAGACGAGGACCATCAGCTTCATCTCAAATGGGCATGAATGGCTCTTCA
TCAATGATGCCAACACTTCAGGCTTCTGGATTTGGTGGAATTTCTGATCAAGTAAAATAT
GCAATTTTGGCGCAACAGTTGAAAGCACGCGATAGTCCTAAAACAATGTTATCAAATTCA
TTTCCACCACTACCATTACCATTACAAACACAATTGACAGTTGATGATGAAGAAATAATC
AGTAATAAAAAATTACCAGAGAAAAACAACACTCCAGCACATCCAGATGATGATGATCCA
CAATTAATTATTGATGAAGATTTCAATGCCGAAGATTTGAGTAAATCATCGATGGAGAGA
AAAATTCTGCTGCACGCAAAGTAG
>g11887.t1 Gene=g11887 Length=1147
MEQIDVAYNNSNSNIKMERRTSTNSESSIEQTEVSSSNKTLSTSDANSSLALKTSQDSDN
VESDENEDYLNNNTRKSNNKNDDGGNESSSVMSHRTNTKDTIVRRDNLSKLMDKMLQKKI
MSVATRHNNNNNHSSEENLNDAENERQNDSMTKDDTTKYVCPICEAVSTTQHDFTNHIRN
HNNTRDSSDDSSSFTCRICSKVLSSASSLDRHVLVHTGERPFNCKFCNLTFTTNGNMHRH
MRTHKQPQHDRESYESDGSTDSSGSSNRKVSNYSNKRKSADDEHTNKRKIRAVNYNNNTI
TSPNFLQQQQNQKFCCPVCIRNDFPSMISLENHMDKEHPTIPAKCRHCEMVFKSHKALNA
HRCGHNKSNNVQQGFGDLSSIIDFSCEKFPLIAQKMCEQSIRTPITNQKYECRICFRAFP
CASAVEIHMRECSDSVTSNKRRRSRSETSVDDEEVRRDDFFANLALQNRPPSSTSSIDKS
FSNKTMVIKQEICETSPYLQYFNEARDFADIESIIKATSSGGLEKPIPEKDQHLYNREEE
EAQDAFTQEFRKMKLRGEFPCRLCTMVFPNLRALKGHNRVHLSASGPGPYRCNMCTFSIN
DKQALIRHMRNHNGDRPYECALCNYAFTTKANCERHLRNRHGKLTREDVKRAIIYHPSED
SSVDDHSKKIALYAQNNRYNRSNDDEDEEENDDELDPSGRSTPVSHLKDILQSRKDDSPS
RIQVKSLEKLKSQQNFENDIEEELNESAQRSGVDLSMDVLDLSKKTDSFAHNNGNDASGE
DESDQERNNNDDDDELHPEIPKFDLGMFEKSFLMQQQLFTEALPKLDPAQMFNLAQMYRT
FGFPTPGFPIHPALFLQNPLLLNDTMKNFFQKDLMPPTPPSSNNNATTNTGSMSGGSMIV
NPFVSPDSSPTAPPNQQTRIDQSPITNSIPVPPFPPTPQESPKKVSTPNSSNINLANHSG
PVKMVIKNGVLMPKQKQRRYRTERPFACEHCSARFTLRSNMERHIKQQHPQFWAQRQRGN
HGLMRRGPSASSQMGMNGSSSMMPTLQASGFGGISDQVKYAILAQQLKARDSPKTMLSNS
FPPLPLPLQTQLTVDDEEIISNKKLPEKNNTPAHPDDDDPQLIIDEDFNAEDLSKSSMER
KILLHAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g11887.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 144 | 219 | 2.6E-12 |
| 12 | g11887.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 220 | 249 | 2.0E-8 |
| 15 | g11887.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 268 | 373 | 1.2E-5 |
| 14 | g11887.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 528 | 612 | 3.5E-11 |
| 11 | g11887.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 613 | 669 | 6.2E-7 |
| 10 | g11887.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 967 | 1020 | 2.1E-7 |
| 36 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 106 | - |
| 45 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 57 | - |
| 35 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 97 | - |
| 40 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 124 | 153 | - |
| 42 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 138 | 153 | - |
| 48 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 289 | - |
| 39 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 258 | 273 | - |
| 37 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 274 | 289 | - |
| 43 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 674 | 722 | - |
| 38 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 771 | 796 | - |
| 41 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 777 | 796 | - |
| 34 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 906 | 960 | - |
| 49 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 906 | 927 | - |
| 33 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 928 | 942 | - |
| 44 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 943 | 958 | - |
| 46 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1102 | 1119 | - |
| 47 | g11887.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1102 | 1121 | - |
| 6 | g11887.t1 | PANTHER | PTHR46451 | RAS-RESPONSIVE ELEMENT-BINDING PROTEIN 1 | 57 | 521 | 5.5E-211 |
| 4 | g11887.t1 | PANTHER | PTHR46451 | RAS-RESPONSIVE ELEMENT-BINDING PROTEIN 1 | 537 | 666 | 5.5E-211 |
| 5 | g11887.t1 | PANTHER | PTHR46451 | RAS-RESPONSIVE ELEMENT-BINDING PROTEIN 1 | 720 | 1052 | 5.5E-211 |
| 3 | g11887.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 159 | 181 | 0.0041 |
| 1 | g11887.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 222 | 244 | 0.0026 |
| 2 | g11887.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 590 | 612 | 0.0033 |
| 21 | g11887.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 196 | 216 | - |
| 20 | g11887.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 224 | 244 | - |
| 19 | g11887.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 345 | 365 | - |
| 16 | g11887.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 561 | 581 | - |
| 17 | g11887.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 592 | 612 | - |
| 22 | g11887.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 620 | 641 | - |
| 18 | g11887.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 988 | 1009 | - |
| 54 | g11887.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 159 | 186 | 8.808 |
| 51 | g11887.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 194 | 221 | 14.295 |
| 50 | g11887.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 222 | 249 | 10.907 |
| 55 | g11887.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 559 | 586 | 9.12 |
| 56 | g11887.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 590 | 617 | 12.778 |
| 53 | g11887.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 618 | 641 | 9.972 |
| 52 | g11887.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 986 | 1009 | 10.034 |
| 28 | g11887.t1 | SMART | SM00355 | c2h2final6 | 159 | 181 | 0.0044 |
| 32 | g11887.t1 | SMART | SM00355 | c2h2final6 | 194 | 216 | 0.0056 |
| 30 | g11887.t1 | SMART | SM00355 | c2h2final6 | 222 | 244 | 0.0013 |
| 24 | g11887.t1 | SMART | SM00355 | c2h2final6 | 314 | 338 | 7.8 |
| 25 | g11887.t1 | SMART | SM00355 | c2h2final6 | 343 | 365 | 7.7 |
| 27 | g11887.t1 | SMART | SM00355 | c2h2final6 | 410 | 430 | 44.0 |
| 26 | g11887.t1 | SMART | SM00355 | c2h2final6 | 559 | 581 | 0.023 |
| 31 | g11887.t1 | SMART | SM00355 | c2h2final6 | 590 | 612 | 0.0012 |
| 29 | g11887.t1 | SMART | SM00355 | c2h2final6 | 618 | 641 | 0.0024 |
| 23 | g11887.t1 | SMART | SM00355 | c2h2final6 | 986 | 1009 | 0.011 |
| 7 | g11887.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 194 | 244 | 1.35E-14 |
| 8 | g11887.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 589 | 638 | 1.29E-12 |
| 9 | g11887.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 977 | 1009 | 1.53E-5 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K20210 (ras-responsive element-binding protein 1)
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.
