General information for g5009.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Restin-like protein.
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.t13 | TTS | g5009.t13 | 6407996 | 6407996 |
| chr_2 | g5009 | g5009.t13 | isoform | g5009.t13 | 6408876 | 6412306 |
| chr_2 | g5009 | g5009.t13 | exon | g5009.t13.exon1 | 6408876 | 6409778 |
| chr_2 | g5009 | g5009.t13 | cds | g5009.t13.CDS1 | 6409605 | 6409778 |
| chr_2 | g5009 | g5009.t13 | exon | g5009.t13.exon2 | 6409854 | 6409964 |
| chr_2 | g5009 | g5009.t13 | cds | g5009.t13.CDS2 | 6409854 | 6409964 |
| chr_2 | g5009 | g5009.t13 | exon | g5009.t13.exon3 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t13 | cds | g5009.t13.CDS3 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t13 | exon | g5009.t13.exon4 | 6411368 | 6411551 |
| chr_2 | g5009 | g5009.t13 | cds | g5009.t13.CDS4 | 6411368 | 6411551 |
| chr_2 | g5009 | g5009.t13 | exon | g5009.t13.exon5 | 6411616 | 6411781 |
| chr_2 | g5009 | g5009.t13 | cds | g5009.t13.CDS5 | 6411616 | 6411781 |
| chr_2 | g5009 | g5009.t13 | exon | g5009.t13.exon6 | 6411845 | 6412078 |
| chr_2 | g5009 | g5009.t13 | cds | g5009.t13.CDS6 | 6411845 | 6412078 |
| chr_2 | g5009 | g5009.t13 | exon | g5009.t13.exon7 | 6412150 | 6412306 |
| chr_2 | g5009 | g5009.t13 | cds | g5009.t13.CDS7 | 6412150 | 6412264 |
| chr_2 | g5009 | g5009.t13 | TSS | g5009.t13 | NA | NA |
Sequences
>g5009.t13 Gene=g5009 Length=1821
TCAGATCATGGAGCAGATTTAACGACAGACACAGATAGTTTTATGATAGGAAATCGAGTT
TATGTTGGAGGAGTTAAACCCGGTCGTATTACTTTTATTGGCGAAGTTCATTTCGCCCCG
GGTGAATGGGCTGGAGTTGTTTTAGATGAGCCAGAAGGCAAAAATGATGGTGCAGTTAGT
GGAAAACGCTATTTTCAGTGTGAACCTAAAAAGGGAATATTTTCACGCCTCACACGACTA
ACTCGTGAACCATTATCATCAACCACAACTGATGGTCCATTAAGTACAGATTATAGCTTC
CGTTCATTTACATCACCACTTCGAAACACATCGGGAAATACATCACCAACACAGAGTGTT
TCTAGTGTCTCTAAAACAGCAGCTGGAACAAAAATTATTCCCGAAATAAATGATCGTGTT
ATTGTCAAGAGTGCAACTGGAAGTCGTGCTGGAATTCTTCGTTATCGTGGAGAGCCAGCA
TTTGCTAGTGGTATTTGGTGTGGTGTTGAATATGAAGAGCCTGTTGGCAAAAATGACGGA
TCAGTTAGTGGACAAAGATATTTCAAATGCGCACCCAATCATGGAATTTTTGTGCCTGAA
GGAAAGGTTGTTTTATCACCATTAGCACGAAAAATGCGCCTTTCAAGACAAAATTCACAA
GAATCGTTAACATCAAACATTACACTTAACAGCTTGGCTTCGACAAATACTTCAAAATTG
CGGTTAAATGCAACACAAAAGCGCCTATCGACACTTAATAAGTCACCATCGGCAACGTCA
ACACCAAAACCCTCGTTCTCGTTGCAGGACATTTTACGAGAGAAATCGAATCATATTGAA
CAAATCATGAAAGAACGAGATATTGAACGTGAAGAAATGGCAGCTCAAACAGTTCTTTAT
CAAAAGAATCTTAATCAGACATTGTCTTATTTACAAAAGAGTCCAAGTCCTGACGTTGAA
GAACATATTGGAAGATGGGCTACATATATTCGACAGAGAAGTGAACACATTGATGACTTG
AGACGACAATTCACAGGTTGGACTGGCAATCACGAGAGACATTGCATTCTTCATGATGTC
TTTTTGACATAAAATAACAACTGATCTAATGAAAAGTGAAAATTATTTTCTAACATTTAA
GAAGTTTTTTTTACATACGTATGATTTAATAAAATGTTATTGCAAGGGTTAGTCATATTT
TCTTGTCAGCCCTTGGCTTAATTTCTTCTTTCAGCTTGCATTTCTTATTTTCATAAAATA
TTTAGCATCGCTACTAACCATTAATTTTCAATATAAGAATGAATTTTTTGTTCTTGGAAA
TTTTGGTTCTCAAAATTTGTTTTTTTACGAAACACTCCTTTGAAAGAGAAATTCTGTAAT
GTAATTCTTTCTTAATCTTTAAAGTAATGAAAAAAAGATTATGAAAGAAACTGTTGTTTG
ATTAAAAAATTTGTTTTATGTCCATAGTCAATAGAAATAAATTCGTTTTGTATTTGCTTA
GCTAACTCTTTACTAATTCTTTTATTAACTTTTTGATTACAAAAATAAAGAAATGTCACA
AAATCAGCTATTCTTTTAATTTGATTTAAATTTTTATCTTTTGAGTTCATGTGGGTTTGT
TTAAAATAAAGAATAAAACATCCATATTTGTAGATGTTTAAAATATTTATGTAATTGTTT
CCAAAACACTTTCTCTCCATAATCACTCCATATTTTTCTCTTTTTCAGTCAGACAGACAC
AGATTAAAGAAATTATTATCATACTATATTTCAATAAATACCATTTTTATCAACTCAGTT
GAGCATTTATTATGACATTCA
>g5009.t13 Gene=g5009 Length=349
MIGNRVYVGGVKPGRITFIGEVHFAPGEWAGVVLDEPEGKNDGAVSGKRYFQCEPKKGIF
SRLTRLTREPLSSTTTDGPLSTDYSFRSFTSPLRNTSGNTSPTQSVSSVSKTAAGTKIIP
EINDRVIVKSATGSRAGILRYRGEPAFASGIWCGVEYEEPVGKNDGSVSGQRYFKCAPNH
GIFVPEGKVVLSPLARKMRLSRQNSQESLTSNITLNSLASTNTSKLRLNATQKRLSTLNK
SPSATSTPKPSFSLQDILREKSNHIEQIMKERDIEREEMAAQTVLYQKNLNQTLSYLQKS
PSPDVEEHIGRWATYIRQRSEHIDDLRRQFTGWTGNHERHCILHDVFLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5009.t13 | Coils | Coil | Coil | 258 | 278 | - |
| 7 | g5009.t13 | Gene3D | G3DSA:2.30.30.190 | - | 1 | 81 | 3.4E-30 |
| 8 | g5009.t13 | Gene3D | G3DSA:2.30.30.190 | - | 96 | 197 | 7.4E-28 |
| 3 | g5009.t13 | PANTHER | PTHR18916:SF79 | RESTIN HOMOLOG | 1 | 297 | 4.5E-82 |
| 4 | g5009.t13 | PANTHER | PTHR18916 | DYNACTIN 1-RELATED MICROTUBULE-BINDING | 1 | 297 | 4.5E-82 |
| 2 | g5009.t13 | Pfam | PF01302 | CAP-Gly domain | 2 | 65 | 5.8E-22 |
| 1 | g5009.t13 | Pfam | PF01302 | CAP-Gly domain | 122 | 189 | 2.0E-23 |
| 10 | g5009.t13 | ProSitePatterns | PS00845 | CAP-Gly domain signature. | 20 | 51 | - |
| 11 | g5009.t13 | ProSitePatterns | PS00845 | CAP-Gly domain signature. | 143 | 174 | - |
| 15 | g5009.t13 | ProSiteProfiles | PS50245 | CAP-Gly domain profile. | 20 | 62 | 17.73 |
| 14 | g5009.t13 | ProSiteProfiles | PS50245 | CAP-Gly domain profile. | 143 | 185 | 18.036 |
| 13 | g5009.t13 | SMART | SM01052 | CAP_GLY_2 | 2 | 67 | 1.4E-28 |
| 12 | g5009.t13 | SMART | SM01052 | CAP_GLY_2 | 122 | 190 | 4.4E-31 |
| 6 | g5009.t13 | SUPERFAMILY | SSF74924 | Cap-Gly domain | 2 | 84 | 1.83E-30 |
| 5 | g5009.t13 | SUPERFAMILY | SSF74924 | Cap-Gly domain | 121 | 203 | 1.96E-29 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5009/g5009.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t13.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. There were no conditions that were differentially expressed