General information for g5009.t3
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.t3 | isoform | g5009.t3 | 6404447 | 6408876 |
| chr_2 | g5009 | g5009.t3 | exon | g5009.t3.exon1 | 6404447 | 6404708 |
| chr_2 | g5009 | g5009.t3 | cds | g5009.t3.CDS1 | 6404447 | 6404708 |
| chr_2 | g5009 | g5009.t3 | exon | g5009.t3.exon2 | 6404764 | 6408340 |
| chr_2 | g5009 | g5009.t3 | cds | g5009.t3.CDS2 | 6404764 | 6408340 |
| chr_2 | g5009 | g5009.t3 | exon | g5009.t3.exon3 | 6408404 | 6408479 |
| chr_2 | g5009 | g5009.t3 | cds | g5009.t3.CDS3 | 6408404 | 6408479 |
| chr_2 | g5009 | g5009.t3 | exon | g5009.t3.exon4 | 6408736 | 6408876 |
| chr_2 | g5009 | g5009.t3 | cds | g5009.t3.CDS4 | 6408736 | 6408876 |
| chr_2 | g5009 | g5009.t3 | TSS | g5009.t3 | NA | NA |
| chr_2 | g5009 | g5009.t3 | TTS | g5009.t3 | NA | NA |
Sequences
>g5009.t3 Gene=g5009 Length=4056
ATGTTCTCTATCTTTTTTTATGGTTCGCAGTATAAAGAAAAGTTGACTCATCTTCAAAAG
CTTCTTGAAGACGAACGAAAGAAAAGTGAAGATCTTCAATTTACTATAGATGAGGCACAA
ACAAACGCTGATGAAAATGAGCTCACACTTCGCGAGAAAATTAAACAATTAGAGCAAATT
TTGAAGCAGCAAACAAAGCAAGGTGCAGGTGATTTCGTTATCGACACTTCACAGAATGAT
GAACTTATTTCAAAACTTCGGATTGAAGTTGATGAACTCAAACAAAAATTACATAATGCA
GAATCACTCAAATCGACATTGGAGAATCAAATACAGTCGTTGAATGAGAAAATTACTGAT
TATAGTAATGAGTTGGAGCTCAAATCTTCTGCCAATGATGCAATTGAAAAGGTTTTCAAA
GAAGAAATTGATTATCTTCAAGGTCGAATCAATGAATTAGAAAAGGAAGTGTCTGACAAA
TCATCACAATTGGAGAATGATAAAGAAAATTTATCTAAAATCGAGTGCTCTTATAATGAA
AAATTATCATTACTTCAAAAAGAAATAGAAGAAAAAATAAATAATGAAAATTTACATGCC
AGTGAATTAGATGCAAAAAATAAAGAAATTGACTCGCTCAAGTCTGATATTGAAAAGCTC
ACTAGTTCTGACCTTGGTGCACAAGAAGTCATAGGTAAAAAAGAAATTGAGATTCAAAAA
CTGACTGAAACTTTGCAAACAAAAGAATTCTCTATTATTGAACTGTCAAGTGAATTAGGA
AAAAAGATTGATGAAGTTACTGCACGCGATAATGAGATTGAAAATTTACAAAAATCTCTA
AAAATACTTGAAAATGAGAAAGAAAATAACAAATCCAATTGTGAACAATATTTAAAAGAT
ATTCAAAAAGGACTTGAAGAAATTTCACATTACAAGACTCAAATAGATACACAAGTTTCA
GAAATTTCATCACTTAAATCTGAATTGCAACGTATGGAAAAGATTGTTAATGATTTAAAT
GAAAATATTCTAAAACATCAAGCCAATGAAGAAGTTTTAACATCCAAAGTAACTGACTTG
TCTGAATCTAAAGTAAAACTCGAAAATGATCTCATTTCAAAAGACAAAGAGATTGCAGAT
GCATTAGAGACTAAACAGAAATTGATTCATGAGCTTGAAGAAGTCAAAAAATGTATGAGC
GGTCTCGATGCAGAAGCACAAGGAAATATTAGTCTCTTGAATGAAAAAGACTCTTTGATT
AAGAACTTAACAAAAGACTTGAATGACTTGAAAGAAACGAGTCAGCAAGAAGTTAAACAA
CTTTTGATCGAAAAAAGTTCTCTTGAAACCAAATTTGAAGAAAGTCAAAAGCTTTTTAAT
GAACAGATTACAAAAGAGAAAGTAGAACATGATGCTGAAAAGGATAAATTGAAAACTACA
ATTGATGAGTTTGAGAAAATAATCAAAGAGAAAGATGCTCGTATGGAAGTTATGGATAAA
AATTCACAATTATTGGAAGAAACAAAAGAAAAATTAGAGAAATCTTTGACTGATTATGAA
AGTAAACTTAATGAGAATTTGACAAAATTAGGTAAATTAGAAAAAGAGCATACCGATACA
TTATTGCAATTCAATAAACTACAATCTCAATATAACGAAACTTCACAAAAGCTTCAAGAA
TTCGAAATAACAACTAAAAAGCTTCAAGATGACAAGAGCGCATTAGATATTGATAACAAA
GATTTGAATCGCAAACTTGGAGCACAAGATGAGAAAATCACACAATTGTCAGAGCAGAAA
TTAAAACTTCAAGAGGAACTTGATTCATATAAAACTTCATCACTCGATGCAAATAGTGAA
CTTAAGAAACTACATGACAGTTTGAAGGAGAAACAATTAGCTTTTGAAAACTATCAAGCA
AATGCTGATAAAAACAATATCGAATTACAACGTCGAATTGATGAACTTGAAAATCAACGT
GACACTGCCAATCAAATGTGTACAAAATTAAAGAGTGAATTAGATACTCTCAATCAACAG
AAAATTGAAAATGAAAATATTCTCAATACTGATTTACAAAATATTAAAGCTAGCACTGAA
GAAGAGAGAGCTAATTTAGTAAGTGAAATAAATAATTTAAGAGCTTCTTTTGAAAATGAG
AGAACAGAATTGAAAAAATGTAATAATGAGCTAGCAGAAGTGTCTGAAAAATGCAAAAAT
GAGCTTGAGGCTAAAATTAAAAGTCTTAATGAAATTCTTGAAGATTTACGTAAAGAATTA
GATGGTGCACGTGCAGAAACTAAAAATTCAGAGTCACGTTTTGGTTCTGCTATTGATGAG
TTGAAATCAAAAGAATCTCAACTCATTGAAGAACTATCAAAAGAACGTGATGAAAGTGAT
AAGCATAAAGCGAAAATTGAAGAATTACAAGCAGCTAAAGATATTCAAAAGAATGAATAT
GAGGAAAAATTGTCAATTGAAAAGGCAAAGATAAAGAAACTCGAAGAAGAGCTTTTTGTT
CAAATTGAACAACATAAATTAGCTTCGGCAGGTAATGAAGAGAAAGTGAAAATTCTTGAC
GATTTTCAAGCGAAATGTTTTGCACATGAACAAAAGATATCTGATTTGAGCAATCAAATT
CAAAATGAAATTTCATCAAAAGCCAAATTAGAAGATAGCTTAAAAGAGCTTCATCAGAAG
CTTCGTGAAATTGAAGAAGAACAAGTTGATTTGGTTAGCAAAAAAGAAGAATATAAGGCA
AAAACAATTGAACAGCAAGAGATGATAAATGAATTGATGCAAAGAAGAAAAAGTCTTGAT
GAAAAACTTTTACTTGAAAAGAAAGATTCAGAGTTATTTAAATCTGAATCCGATATCAAA
ATTAAAGAAATGCAGCAAAAATTAAATGAACTCAATCAAATGGTCGCCAAAAAAGACTTT
GAAAAAGAAGAAATATTAACTAGTTTAAAGCTTCGTGATGAAAAGCTAAGTCAATTATAT
GATTCTATAAAGCAACAAGATAGAAAATTGCAAGATGAAATCGATAGCATACAAAAAGAG
ATGAAATCAAAGGATGATGAAATAATTAAAATGGCTAATGAAAACAATGTAAAAGATGAT
TTGCTCAATGATTTACGCAATACTGTTGAAAATCTTAAAACGTGCCTTAATACAATGAAT
GACGAAAAAACTTTTAGTAAAGATGCAGTTGAAGAGCTCAATCAAAATATTCATTCACGT
GATGAAAAGATCAATGAATTATCATTAGAAATTCACTCTTTAAAATCTAATCTCAAGGAA
AAGGATGATCAACTCAAAAATGTCTATGCTATAAAAAGCAAAGTTGAATCAGAGTCAAGA
CAACGCATTGATGATTTAATGGAGCAGCTAAATATTTTAGAAGAAGTCAAAACTAAAGAA
TTTTCTGAAATAAATGAAAAGCTTTCTCAACTGACGACACAAGTTAGTATATATCAGACC
GAATCAGAGTCTTCATGTGTTAGCGAAAAAGATATTGAAAACATGCGTCAAGAATATCTT
ATGAAAATTAGAGATTTGGAAATGTCTGAGACTGAGCTTCAAATTACAAATCAAGCATTA
AAACGACAATTGGAAGAAATTCAAAGCACTACATCGCTTGTTCCAAAAATGGAAGGAGGT
GATCAAGATTTGGTTGAACATATCGAATTTTTGAACTCAATCATAGCAGATATGCATAAG
AAAAATTTGAAATTGACGAAGCAAGTCCAATCGATGGAAGTTGGTTCATCAAAATCAAAT
ACTTCATTTAAAGAGAACGATTTCGATATGAAATTCTTGGAAAAGAAGCAATTACCACCA
CCTCGAATGTATTGCGATATCTGTGAAGTTTTTGATGCTCACGAGACAGAAGACTGTCCA
ACACAATGCTCATCAATTGACCTTGATGCACCGGCTGTCAAGCGAGAAGAAAAGAAGGAG
CGCAAGAAGCCACCGCCAAGGAAATATTGCGATTTTTGTGAAATATTCGATGCTCATGAA
ACTGAAGAATGCCCAAACAACGATGAAACATTTTAA
>g5009.t3 Gene=g5009 Length=1351
MFSIFFYGSQYKEKLTHLQKLLEDERKKSEDLQFTIDEAQTNADENELTLREKIKQLEQI
LKQQTKQGAGDFVIDTSQNDELISKLRIEVDELKQKLHNAESLKSTLENQIQSLNEKITD
YSNELELKSSANDAIEKVFKEEIDYLQGRINELEKEVSDKSSQLENDKENLSKIECSYNE
KLSLLQKEIEEKINNENLHASELDAKNKEIDSLKSDIEKLTSSDLGAQEVIGKKEIEIQK
LTETLQTKEFSIIELSSELGKKIDEVTARDNEIENLQKSLKILENEKENNKSNCEQYLKD
IQKGLEEISHYKTQIDTQVSEISSLKSELQRMEKIVNDLNENILKHQANEEVLTSKVTDL
SESKVKLENDLISKDKEIADALETKQKLIHELEEVKKCMSGLDAEAQGNISLLNEKDSLI
KNLTKDLNDLKETSQQEVKQLLIEKSSLETKFEESQKLFNEQITKEKVEHDAEKDKLKTT
IDEFEKIIKEKDARMEVMDKNSQLLEETKEKLEKSLTDYESKLNENLTKLGKLEKEHTDT
LLQFNKLQSQYNETSQKLQEFEITTKKLQDDKSALDIDNKDLNRKLGAQDEKITQLSEQK
LKLQEELDSYKTSSLDANSELKKLHDSLKEKQLAFENYQANADKNNIELQRRIDELENQR
DTANQMCTKLKSELDTLNQQKIENENILNTDLQNIKASTEEERANLVSEINNLRASFENE
RTELKKCNNELAEVSEKCKNELEAKIKSLNEILEDLRKELDGARAETKNSESRFGSAIDE
LKSKESQLIEELSKERDESDKHKAKIEELQAAKDIQKNEYEEKLSIEKAKIKKLEEELFV
QIEQHKLASAGNEEKVKILDDFQAKCFAHEQKISDLSNQIQNEISSKAKLEDSLKELHQK
LREIEEEQVDLVSKKEEYKAKTIEQQEMINELMQRRKSLDEKLLLEKKDSELFKSESDIK
IKEMQQKLNELNQMVAKKDFEKEEILTSLKLRDEKLSQLYDSIKQQDRKLQDEIDSIQKE
MKSKDDEIIKMANENNVKDDLLNDLRNTVENLKTCLNTMNDEKTFSKDAVEELNQNIHSR
DEKINELSLEIHSLKSNLKEKDDQLKNVYAIKSKVESESRQRIDDLMEQLNILEEVKTKE
FSEINEKLSQLTTQVSIYQTESESSCVSEKDIENMRQEYLMKIRDLEMSETELQITNQAL
KRQLEEIQSTTSLVPKMEGGDQDLVEHIEFLNSIIADMHKKNLKLTKQVQSMEVGSSKSN
TSFKENDFDMKFLEKKQLPPPRMYCDICEVFDAHETEDCPTQCSSIDLDAPAVKREEKKE
RKKPPPRKYCDFCEIFDAHETEECPNNDETF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5009.t3 | Coils | Coil | Coil | 22 | 67 | - |
| 11 | g5009.t3 | Coils | Coil | Coil | 83 | 131 | - |
| 14 | g5009.t3 | Coils | Coil | Coil | 136 | 170 | - |
| 18 | g5009.t3 | Coils | Coil | Coil | 203 | 223 | - |
| 13 | g5009.t3 | Coils | Coil | Coil | 266 | 300 | - |
| 8 | g5009.t3 | Coils | Coil | Coil | 315 | 349 | - |
| 19 | g5009.t3 | Coils | Coil | Coil | 413 | 458 | - |
| 6 | g5009.t3 | Coils | Coil | Coil | 460 | 536 | - |
| 10 | g5009.t3 | Coils | Coil | Coil | 544 | 613 | - |
| 9 | g5009.t3 | Coils | Coil | Coil | 621 | 680 | - |
| 16 | g5009.t3 | Coils | Coil | Coil | 689 | 773 | - |
| 12 | g5009.t3 | Coils | Coil | Coil | 778 | 837 | - |
| 17 | g5009.t3 | Coils | Coil | Coil | 859 | 949 | - |
| 21 | g5009.t3 | Coils | Coil | Coil | 954 | 984 | - |
| 23 | g5009.t3 | Coils | Coil | Coil | 1000 | 1034 | - |
| 20 | g5009.t3 | Coils | Coil | Coil | 1042 | 1104 | - |
| 22 | g5009.t3 | Coils | Coil | Coil | 1116 | 1136 | - |
| 7 | g5009.t3 | Coils | Coil | Coil | 1183 | 1210 | - |
| 3 | g5009.t3 | PANTHER | PTHR18916:SF44 | CAP-GLY DOMAIN-CONTAINING LINKER PROTEIN 1 | 1184 | 1351 | 4.9E-21 |
| 4 | g5009.t3 | PANTHER | PTHR18916 | DYNACTIN 1-RELATED MICROTUBULE-BINDING | 1184 | 1351 | 4.9E-21 |
| 2 | g5009.t3 | Pfam | PF16641 | CLIP1 zinc knuckle | 1282 | 1299 | 6.9E-8 |
| 1 | g5009.t3 | Pfam | PF16641 | CLIP1 zinc knuckle | 1327 | 1344 | 2.6E-5 |
| 5 | g5009.t3 | SUPERFAMILY | SSF90257 | Myosin rod fragments | 505 | 616 | 1.28E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5009/g5009.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t3.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.
