General information for g5009.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative CAP-Gly domain-containing linker protein 1.
Parent gene
- The parent gene g5009 is located on chr_2: 6422853..6423614 (- 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_2 | g5009 | g5009.t2 | isoform | g5009.t2 | 6404447 | 6408876 |
| chr_2 | g5009 | g5009.t2 | exon | g5009.t2.exon1 | 6404447 | 6404708 |
| chr_2 | g5009 | g5009.t2 | cds | g5009.t2.CDS1 | 6404447 | 6404708 |
| chr_2 | g5009 | g5009.t2 | exon | g5009.t2.exon2 | 6404764 | 6408340 |
| chr_2 | g5009 | g5009.t2 | cds | g5009.t2.CDS2 | 6404764 | 6408340 |
| chr_2 | g5009 | g5009.t2 | exon | g5009.t2.exon3 | 6408404 | 6408479 |
| chr_2 | g5009 | g5009.t2 | cds | g5009.t2.CDS3 | 6408404 | 6408479 |
| chr_2 | g5009 | g5009.t2 | exon | g5009.t2.exon4 | 6408617 | 6408634 |
| chr_2 | g5009 | g5009.t2 | cds | g5009.t2.CDS4 | 6408617 | 6408634 |
| chr_2 | g5009 | g5009.t2 | exon | g5009.t2.exon5 | 6408736 | 6408876 |
| chr_2 | g5009 | g5009.t2 | cds | g5009.t2.CDS5 | 6408736 | 6408876 |
| chr_2 | g5009 | g5009.t2 | TSS | g5009.t2 | NA | NA |
| chr_2 | g5009 | g5009.t2 | TTS | g5009.t2 | NA | NA |
Sequences
>g5009.t2 Gene=g5009 Length=4074
ATGTTCTCTATCTTTTTTTATGGTTCGCAGTATAAAGAAAAGTTGACTCATCTTCAAAAG
CTTCTTGAAGACGAACGAAAGAAAAGTGAAGATCTTCAATTTACTATAGATGAGGCACAA
ACAAACGCTGATGAAAATGAGTCGAAAAACACGACTGAACTCACACTTCGCGAGAAAATT
AAACAATTAGAGCAAATTTTGAAGCAGCAAACAAAGCAAGGTGCAGGTGATTTCGTTATC
GACACTTCACAGAATGATGAACTTATTTCAAAACTTCGGATTGAAGTTGATGAACTCAAA
CAAAAATTACATAATGCAGAATCACTCAAATCGACATTGGAGAATCAAATACAGTCGTTG
AATGAGAAAATTACTGATTATAGTAATGAGTTGGAGCTCAAATCTTCTGCCAATGATGCA
ATTGAAAAGGTTTTCAAAGAAGAAATTGATTATCTTCAAGGTCGAATCAATGAATTAGAA
AAGGAAGTGTCTGACAAATCATCACAATTGGAGAATGATAAAGAAAATTTATCTAAAATC
GAGTGCTCTTATAATGAAAAATTATCATTACTTCAAAAAGAAATAGAAGAAAAAATAAAT
AATGAAAATTTACATGCCAGTGAATTAGATGCAAAAAATAAAGAAATTGACTCGCTCAAG
TCTGATATTGAAAAGCTCACTAGTTCTGACCTTGGTGCACAAGAAGTCATAGGTAAAAAA
GAAATTGAGATTCAAAAACTGACTGAAACTTTGCAAACAAAAGAATTCTCTATTATTGAA
CTGTCAAGTGAATTAGGAAAAAAGATTGATGAAGTTACTGCACGCGATAATGAGATTGAA
AATTTACAAAAATCTCTAAAAATACTTGAAAATGAGAAAGAAAATAACAAATCCAATTGT
GAACAATATTTAAAAGATATTCAAAAAGGACTTGAAGAAATTTCACATTACAAGACTCAA
ATAGATACACAAGTTTCAGAAATTTCATCACTTAAATCTGAATTGCAACGTATGGAAAAG
ATTGTTAATGATTTAAATGAAAATATTCTAAAACATCAAGCCAATGAAGAAGTTTTAACA
TCCAAAGTAACTGACTTGTCTGAATCTAAAGTAAAACTCGAAAATGATCTCATTTCAAAA
GACAAAGAGATTGCAGATGCATTAGAGACTAAACAGAAATTGATTCATGAGCTTGAAGAA
GTCAAAAAATGTATGAGCGGTCTCGATGCAGAAGCACAAGGAAATATTAGTCTCTTGAAT
GAAAAAGACTCTTTGATTAAGAACTTAACAAAAGACTTGAATGACTTGAAAGAAACGAGT
CAGCAAGAAGTTAAACAACTTTTGATCGAAAAAAGTTCTCTTGAAACCAAATTTGAAGAA
AGTCAAAAGCTTTTTAATGAACAGATTACAAAAGAGAAAGTAGAACATGATGCTGAAAAG
GATAAATTGAAAACTACAATTGATGAGTTTGAGAAAATAATCAAAGAGAAAGATGCTCGT
ATGGAAGTTATGGATAAAAATTCACAATTATTGGAAGAAACAAAAGAAAAATTAGAGAAA
TCTTTGACTGATTATGAAAGTAAACTTAATGAGAATTTGACAAAATTAGGTAAATTAGAA
AAAGAGCATACCGATACATTATTGCAATTCAATAAACTACAATCTCAATATAACGAAACT
TCACAAAAGCTTCAAGAATTCGAAATAACAACTAAAAAGCTTCAAGATGACAAGAGCGCA
TTAGATATTGATAACAAAGATTTGAATCGCAAACTTGGAGCACAAGATGAGAAAATCACA
CAATTGTCAGAGCAGAAATTAAAACTTCAAGAGGAACTTGATTCATATAAAACTTCATCA
CTCGATGCAAATAGTGAACTTAAGAAACTACATGACAGTTTGAAGGAGAAACAATTAGCT
TTTGAAAACTATCAAGCAAATGCTGATAAAAACAATATCGAATTACAACGTCGAATTGAT
GAACTTGAAAATCAACGTGACACTGCCAATCAAATGTGTACAAAATTAAAGAGTGAATTA
GATACTCTCAATCAACAGAAAATTGAAAATGAAAATATTCTCAATACTGATTTACAAAAT
ATTAAAGCTAGCACTGAAGAAGAGAGAGCTAATTTAGTAAGTGAAATAAATAATTTAAGA
GCTTCTTTTGAAAATGAGAGAACAGAATTGAAAAAATGTAATAATGAGCTAGCAGAAGTG
TCTGAAAAATGCAAAAATGAGCTTGAGGCTAAAATTAAAAGTCTTAATGAAATTCTTGAA
GATTTACGTAAAGAATTAGATGGTGCACGTGCAGAAACTAAAAATTCAGAGTCACGTTTT
GGTTCTGCTATTGATGAGTTGAAATCAAAAGAATCTCAACTCATTGAAGAACTATCAAAA
GAACGTGATGAAAGTGATAAGCATAAAGCGAAAATTGAAGAATTACAAGCAGCTAAAGAT
ATTCAAAAGAATGAATATGAGGAAAAATTGTCAATTGAAAAGGCAAAGATAAAGAAACTC
GAAGAAGAGCTTTTTGTTCAAATTGAACAACATAAATTAGCTTCGGCAGGTAATGAAGAG
AAAGTGAAAATTCTTGACGATTTTCAAGCGAAATGTTTTGCACATGAACAAAAGATATCT
GATTTGAGCAATCAAATTCAAAATGAAATTTCATCAAAAGCCAAATTAGAAGATAGCTTA
AAAGAGCTTCATCAGAAGCTTCGTGAAATTGAAGAAGAACAAGTTGATTTGGTTAGCAAA
AAAGAAGAATATAAGGCAAAAACAATTGAACAGCAAGAGATGATAAATGAATTGATGCAA
AGAAGAAAAAGTCTTGATGAAAAACTTTTACTTGAAAAGAAAGATTCAGAGTTATTTAAA
TCTGAATCCGATATCAAAATTAAAGAAATGCAGCAAAAATTAAATGAACTCAATCAAATG
GTCGCCAAAAAAGACTTTGAAAAAGAAGAAATATTAACTAGTTTAAAGCTTCGTGATGAA
AAGCTAAGTCAATTATATGATTCTATAAAGCAACAAGATAGAAAATTGCAAGATGAAATC
GATAGCATACAAAAAGAGATGAAATCAAAGGATGATGAAATAATTAAAATGGCTAATGAA
AACAATGTAAAAGATGATTTGCTCAATGATTTACGCAATACTGTTGAAAATCTTAAAACG
TGCCTTAATACAATGAATGACGAAAAAACTTTTAGTAAAGATGCAGTTGAAGAGCTCAAT
CAAAATATTCATTCACGTGATGAAAAGATCAATGAATTATCATTAGAAATTCACTCTTTA
AAATCTAATCTCAAGGAAAAGGATGATCAACTCAAAAATGTCTATGCTATAAAAAGCAAA
GTTGAATCAGAGTCAAGACAACGCATTGATGATTTAATGGAGCAGCTAAATATTTTAGAA
GAAGTCAAAACTAAAGAATTTTCTGAAATAAATGAAAAGCTTTCTCAACTGACGACACAA
GTTAGTATATATCAGACCGAATCAGAGTCTTCATGTGTTAGCGAAAAAGATATTGAAAAC
ATGCGTCAAGAATATCTTATGAAAATTAGAGATTTGGAAATGTCTGAGACTGAGCTTCAA
ATTACAAATCAAGCATTAAAACGACAATTGGAAGAAATTCAAAGCACTACATCGCTTGTT
CCAAAAATGGAAGGAGGTGATCAAGATTTGGTTGAACATATCGAATTTTTGAACTCAATC
ATAGCAGATATGCATAAGAAAAATTTGAAATTGACGAAGCAAGTCCAATCGATGGAAGTT
GGTTCATCAAAATCAAATACTTCATTTAAAGAGAACGATTTCGATATGAAATTCTTGGAA
AAGAAGCAATTACCACCACCTCGAATGTATTGCGATATCTGTGAAGTTTTTGATGCTCAC
GAGACAGAAGACTGTCCAACACAATGCTCATCAATTGACCTTGATGCACCGGCTGTCAAG
CGAGAAGAAAAGAAGGAGCGCAAGAAGCCACCGCCAAGGAAATATTGCGATTTTTGTGAA
ATATTCGATGCTCATGAAACTGAAGAATGCCCAAACAACGATGAAACATTTTAA
>g5009.t2 Gene=g5009 Length=1357
MFSIFFYGSQYKEKLTHLQKLLEDERKKSEDLQFTIDEAQTNADENESKNTTELTLREKI
KQLEQILKQQTKQGAGDFVIDTSQNDELISKLRIEVDELKQKLHNAESLKSTLENQIQSL
NEKITDYSNELELKSSANDAIEKVFKEEIDYLQGRINELEKEVSDKSSQLENDKENLSKI
ECSYNEKLSLLQKEIEEKINNENLHASELDAKNKEIDSLKSDIEKLTSSDLGAQEVIGKK
EIEIQKLTETLQTKEFSIIELSSELGKKIDEVTARDNEIENLQKSLKILENEKENNKSNC
EQYLKDIQKGLEEISHYKTQIDTQVSEISSLKSELQRMEKIVNDLNENILKHQANEEVLT
SKVTDLSESKVKLENDLISKDKEIADALETKQKLIHELEEVKKCMSGLDAEAQGNISLLN
EKDSLIKNLTKDLNDLKETSQQEVKQLLIEKSSLETKFEESQKLFNEQITKEKVEHDAEK
DKLKTTIDEFEKIIKEKDARMEVMDKNSQLLEETKEKLEKSLTDYESKLNENLTKLGKLE
KEHTDTLLQFNKLQSQYNETSQKLQEFEITTKKLQDDKSALDIDNKDLNRKLGAQDEKIT
QLSEQKLKLQEELDSYKTSSLDANSELKKLHDSLKEKQLAFENYQANADKNNIELQRRID
ELENQRDTANQMCTKLKSELDTLNQQKIENENILNTDLQNIKASTEEERANLVSEINNLR
ASFENERTELKKCNNELAEVSEKCKNELEAKIKSLNEILEDLRKELDGARAETKNSESRF
GSAIDELKSKESQLIEELSKERDESDKHKAKIEELQAAKDIQKNEYEEKLSIEKAKIKKL
EEELFVQIEQHKLASAGNEEKVKILDDFQAKCFAHEQKISDLSNQIQNEISSKAKLEDSL
KELHQKLREIEEEQVDLVSKKEEYKAKTIEQQEMINELMQRRKSLDEKLLLEKKDSELFK
SESDIKIKEMQQKLNELNQMVAKKDFEKEEILTSLKLRDEKLSQLYDSIKQQDRKLQDEI
DSIQKEMKSKDDEIIKMANENNVKDDLLNDLRNTVENLKTCLNTMNDEKTFSKDAVEELN
QNIHSRDEKINELSLEIHSLKSNLKEKDDQLKNVYAIKSKVESESRQRIDDLMEQLNILE
EVKTKEFSEINEKLSQLTTQVSIYQTESESSCVSEKDIENMRQEYLMKIRDLEMSETELQ
ITNQALKRQLEEIQSTTSLVPKMEGGDQDLVEHIEFLNSIIADMHKKNLKLTKQVQSMEV
GSSKSNTSFKENDFDMKFLEKKQLPPPRMYCDICEVFDAHETEDCPTQCSSIDLDAPAVK
REEKKERKKPPPRKYCDFCEIFDAHETEECPNNDETF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5009.t2 | Coils | Coil | Coil | 22 | 42 | - |
| 20 | g5009.t2 | Coils | Coil | Coil | 53 | 73 | - |
| 23 | g5009.t2 | Coils | Coil | Coil | 89 | 137 | - |
| 15 | g5009.t2 | Coils | Coil | Coil | 142 | 176 | - |
| 14 | g5009.t2 | Coils | Coil | Coil | 209 | 229 | - |
| 11 | g5009.t2 | Coils | Coil | Coil | 272 | 306 | - |
| 22 | g5009.t2 | Coils | Coil | Coil | 321 | 355 | - |
| 6 | g5009.t2 | Coils | Coil | Coil | 419 | 464 | - |
| 18 | g5009.t2 | Coils | Coil | Coil | 466 | 542 | - |
| 24 | g5009.t2 | Coils | Coil | Coil | 550 | 619 | - |
| 21 | g5009.t2 | Coils | Coil | Coil | 627 | 686 | - |
| 16 | g5009.t2 | Coils | Coil | Coil | 695 | 779 | - |
| 13 | g5009.t2 | Coils | Coil | Coil | 784 | 843 | - |
| 8 | g5009.t2 | Coils | Coil | Coil | 865 | 955 | - |
| 19 | g5009.t2 | Coils | Coil | Coil | 960 | 990 | - |
| 10 | g5009.t2 | Coils | Coil | Coil | 1006 | 1040 | - |
| 12 | g5009.t2 | Coils | Coil | Coil | 1048 | 1110 | - |
| 7 | g5009.t2 | Coils | Coil | Coil | 1122 | 1142 | - |
| 9 | g5009.t2 | Coils | Coil | Coil | 1189 | 1216 | - |
| 3 | g5009.t2 | PANTHER | PTHR18916:SF44 | CAP-GLY DOMAIN-CONTAINING LINKER PROTEIN 1 | 1191 | 1357 | 3.0E-20 |
| 4 | g5009.t2 | PANTHER | PTHR18916 | DYNACTIN 1-RELATED MICROTUBULE-BINDING | 1191 | 1357 | 3.0E-20 |
| 1 | g5009.t2 | Pfam | PF16641 | CLIP1 zinc knuckle | 1288 | 1305 | 7.0E-8 |
| 2 | g5009.t2 | Pfam | PF16641 | CLIP1 zinc knuckle | 1333 | 1350 | 2.6E-5 |
| 5 | g5009.t2 | SUPERFAMILY | SSF90257 | Myosin rod fragments | 511 | 622 | 1.39E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5009/g5009.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K10421 (CAP-Gly domain-containing linker 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.
