General information for g5009.t15
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.t15 | isoform | g5009.t15 | 6408876 | 6421462 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon1 | 6408876 | 6409757 |
| chr_2 | g5009 | g5009.t15 | TTS | g5009.t15 | 6409138 | 6409138 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS1 | 6409605 | 6409757 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon2 | 6409854 | 6409964 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS2 | 6409854 | 6409964 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon3 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS3 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon4 | 6411368 | 6411551 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS4 | 6411368 | 6411551 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon5 | 6411616 | 6411781 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS5 | 6411616 | 6411781 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon6 | 6411845 | 6412078 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS6 | 6411845 | 6412078 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon7 | 6412150 | 6412302 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS7 | 6412150 | 6412302 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon8 | 6412791 | 6412853 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS8 | 6412791 | 6412853 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon9 | 6413085 | 6413216 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS9 | 6413085 | 6413216 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon10 | 6413876 | 6413950 |
| chr_2 | g5009 | g5009.t15 | cds | g5009.t15.CDS10 | 6413876 | 6413918 |
| chr_2 | g5009 | g5009.t15 | exon | g5009.t15.exon11 | 6421285 | 6421462 |
| chr_2 | g5009 | g5009.t15 | TSS | g5009.t15 | 6421462 | 6421462 |
Sequences
>g5009.t15 Gene=g5009 Length=2244
AGTTTTACTTTAGACTCGAATATAGTCAGTCACCTTAAAATTTTGCTGGCAATCTATATT
AACAACTTGATAAAAAAAATATTTTACAACCACAACAGATTAAGAGCAAAAAATACGACA
CAAATTAATTTTGAAAAAAAAAAATACTACGAAAAATCCATAAAGCAATTTAAATTAGGT
GAACTCAGTAACAACGACTACGGTGACACAATGCGACGTCAAAGCGATGATTATAAAACA
CACTATTTACCAGATGTAAGTGAAGAAAGCGAATATGACTTGCTATATGACCGTTTTGGA
CTTGGTTATCGCTCATCTAAATCTAAATCACAATCACCTGATCCATTTCGATTGTACAAG
TATTCGCCCGATCGCAAAAGTTCAAGTGGTATATCCTCCTCTGTATCACCAGACTTTTTT
GAAGCCACTGGCAGACGATCAAGCTCAGATCATGGAGCAGATTTAACGACAGACACAGAT
AGTTTTATGATAGGAAATCGAGTTTATGTTGGAGGAGTTAAACCCGGTCGTATTACTTTT
ATTGGCGAAGTTCATTTCGCCCCGGGTGAATGGGCTGGAGTTGTTTTAGATGAGCCAGAA
GGCAAAAATGATGGTGCAGTTAGTGGAAAACGCTATTTTCAGTGTGAACCTAAAAAGGGA
ATATTTTCACGCCTCACACGACTAACTCGTGAACCATTATCATCAACCACAACTGATGGT
CCATTAAGTACAGATTATAGCTTCCGTTCATTTACATCACCACTTCGAAACACATCGGGA
AATACATCACCAACACAGAGTGTTTCTAGTGTCTCTAAAACAGCAGCTGGAACAAAAATT
ATTCCCGAAATAAATGATCGTGTTATTGTCAAGAGTGCAACTGGAAGTCGTGCTGGAATT
CTTCGTTATCGTGGAGAGCCAGCATTTGCTAGTGGTATTTGGTGTGGTGTTGAATATGAA
GAGCCTGTTGGCAAAAATGACGGATCAGTTAGTGGACAAAGATATTTCAAATGCGCACCC
AATCATGGAATTTTTGTGCCTGAAGGAAAGGTTGTTTTATCACCATTAGCACGAAAAATG
CGCCTTTCAAGACAAAATTCACAAGAATCGTTAACATCAAACATTACACTTAACAGCTTG
GCTTCGACAAATACTTCAAAATTGCGGTTAAATGCAACACAAAAGCGCCTATCGACACTT
AATAAGTCACCATCGGCAACGTCAACACCAAAACCCTCGTTCTCGTTGCAGGACATTTTA
CGAGAGAAATCGAATCATATTGAACAAATCATGAAAGAACGAGATATTGAACGTGAAGAA
ATGGCAGCTCAAACAGTTCTTTATCAAAAGAATCTTAATCAGAGTCCAAGTCCTGACGTT
GAAGAACATATTGGAAGATGGGCTACATATATTCGACAGAGAAGTGAACACATTGATGAC
TTGAGACGACAATTCACAGGTTGGACTGGCAATCACGAGAGACATTGCATTCTTCATGAT
GTCTTTTTGACATAAAATAACAACTGATCTAATGAAAAGTGAAAATTATTTTCTAACATT
TAAGAAGTTTTTTTTACATACGTATGATTTAATAAAATGTTATTGCAAGGGTTAGTCATA
TTTTCTTGTCAGCCCTTGGCTTAATTTCTTCTTTCAGCTTGCATTTCTTATTTTCATAAA
ATATTTAGCATCGCTACTAACCATTAATTTTCAATATAAGAATGAATTTTTTGTTCTTGG
AAATTTTGGTTCTCAAAATTTGTTTTTTTACGAAACACTCCTTTGAAAGAGAAATTCTGT
AATGTAATTCTTTCTTAATCTTTAAAGTAATGAAAAAAAGATTATGAAAGAAACTGTTGT
TTGATTAAAAAATTTGTTTTATGTCCATAGTCAATAGAAATAAATTCGTTTTGTATTTGC
TTAGCTAACTCTTTACTAATTCTTTTATTAACTTTTTGATTACAAAAATAAAGAAATGTC
ACAAAATCAGCTATTCTTTTAATTTGATTTAAATTTTTATCTTTTGAGTTCATGTGGGTT
TGTTTAAAATAAAGAATAAAACATCCATATTTGTAGATGTTTAAAATATTTATGTAATTG
TTTCCAAAACACTTTCTCTCCATAATCACTCCATATTTTTCTCTTTTTCAGTCAGACAGA
CACAGATTAAAGAAATTATTATCATACTATATTTCAATAAATACCATTTTTATCAACTCA
GTTGAGCATTTATTATGACATTCA
>g5009.t15 Gene=g5009 Length=434
MRRQSDDYKTHYLPDVSEESEYDLLYDRFGLGYRSSKSKSQSPDPFRLYKYSPDRKSSSG
ISSSVSPDFFEATGRRSSSDHGADLTTDTDSFMIGNRVYVGGVKPGRITFIGEVHFAPGE
WAGVVLDEPEGKNDGAVSGKRYFQCEPKKGIFSRLTRLTREPLSSTTTDGPLSTDYSFRS
FTSPLRNTSGNTSPTQSVSSVSKTAAGTKIIPEINDRVIVKSATGSRAGILRYRGEPAFA
SGIWCGVEYEEPVGKNDGSVSGQRYFKCAPNHGIFVPEGKVVLSPLARKMRLSRQNSQES
LTSNITLNSLASTNTSKLRLNATQKRLSTLNKSPSATSTPKPSFSLQDILREKSNHIEQI
MKERDIEREEMAAQTVLYQKNLNQSPSPDVEEHIGRWATYIRQRSEHIDDLRRQFTGWTG
NHERHCILHDVFLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5009.t15 | Coils | Coil | Coil | 350 | 370 | - |
| 8 | g5009.t15 | Gene3D | G3DSA:2.30.30.190 | - | 76 | 169 | 3.0E-31 |
| 7 | g5009.t15 | Gene3D | G3DSA:2.30.30.190 | - | 188 | 289 | 1.1E-27 |
| 3 | g5009.t15 | PANTHER | PTHR18916:SF79 | RESTIN HOMOLOG | 58 | 381 | 2.9E-87 |
| 4 | g5009.t15 | PANTHER | PTHR18916 | DYNACTIN 1-RELATED MICROTUBULE-BINDING | 58 | 381 | 2.9E-87 |
| 2 | g5009.t15 | Pfam | PF01302 | CAP-Gly domain | 94 | 157 | 8.1E-22 |
| 1 | g5009.t15 | Pfam | PF01302 | CAP-Gly domain | 214 | 281 | 2.9E-23 |
| 11 | g5009.t15 | ProSitePatterns | PS00845 | CAP-Gly domain signature. | 112 | 143 | - |
| 10 | g5009.t15 | ProSitePatterns | PS00845 | CAP-Gly domain signature. | 235 | 266 | - |
| 14 | g5009.t15 | ProSiteProfiles | PS50245 | CAP-Gly domain profile. | 112 | 154 | 17.73 |
| 15 | g5009.t15 | ProSiteProfiles | PS50245 | CAP-Gly domain profile. | 235 | 277 | 18.036 |
| 13 | g5009.t15 | SMART | SM01052 | CAP_GLY_2 | 94 | 159 | 1.4E-28 |
| 12 | g5009.t15 | SMART | SM01052 | CAP_GLY_2 | 214 | 282 | 4.4E-31 |
| 5 | g5009.t15 | SUPERFAMILY | SSF74924 | Cap-Gly domain | 75 | 176 | 1.31E-32 |
| 6 | g5009.t15 | SUPERFAMILY | SSF74924 | Cap-Gly domain | 213 | 295 | 3.93E-29 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5009/g5009.t15; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t15.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