General information for g17040.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Carboxypeptidase N subunit 2.
Parent gene
- The parent gene g17040 is located on chr_4: 12297939..12299240 (+ 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_4 | g17040 | g17040.t12 | isoform | g17040.t12 | 12297430 | 12299240 |
| chr_4 | g17040 | g17040.t12 | exon | g17040.t12.exon1 | 12297430 | 12297587 |
| chr_4 | g17040 | g17040.t12 | TSS | g17040.t12 | 12297450 | 12297450 |
| chr_4 | g17040 | g17040.t12 | exon | g17040.t12.exon2 | 12297807 | 12297942 |
| chr_4 | g17040 | g17040.t12 | cds | g17040.t12.CDS1 | 12297855 | 12297942 |
| chr_4 | g17040 | g17040.t12 | exon | g17040.t12.exon3 | 12298159 | 12299240 |
| chr_4 | g17040 | g17040.t12 | cds | g17040.t12.CDS2 | 12298159 | 12299240 |
| chr_4 | g17040 | g17040.t12 | TTS | g17040.t12 | 12298406 | 12298406 |
Sequences
>g17040.t12 Gene=g17040 Length=1376
ATTATTGAGAGTTCAAGTGAGCGCAAATAGACGTGATTTTGTTTTTGTTAAAAATTATTT
TTTTTGAAATTGTTTTTACAAAATTAAAAAAAAAATTCAAGTTTTTTAAGTTAAAAAATT
GTAAATTGTTTTTTTAATGAAAAATAAAAATAAAAAATACCTTTAAAATGTTTTTCATCA
ATTTTTTTTATTTTAACTGCGCATTTATGGCGATTTGTTTTGCTTTTGGAAGCAGTGAAT
TAAAATGTCAACTTGATTATAAACTTGTAGACAATAACTGCATCGAAAAAATGAACATGA
TTGATGGAATCATAACACAAGAAAAATGCTGTACGGTTACAAAATGTGCAATTCCTGATT
ATAAAAATGGAAGCTATCAACAATTTAGTGTCAACGAGGAAACGAAAATTACTGAAAATG
ATGCAGAAATCAAACCTAACTATAAAAGCAATAAAATTGAAATTTTTTATATTGGAAAAA
AATGCAGTGGTGAAAAAGTTGACATTTTTTATCTTCCAATAAAAGTGAATGAAATTTTTC
CAAATTTAATTTCTTACACTGCATATCGAACTAAAGTTAAACATTTGACAAAAGAAAATT
TCAAAGGAATGAAAAAATTATTCTATTTAGGTTTTGTTAATAATGAAATTGAAACAATTG
ATGATGACACTTTTGATGATTTGAATGAGTTAGAATATTTAAATTTGGAATCTAACAAAA
TGAAAATTTTAAATCCAAGAATTTTTATGAATAATCTAAAACTTGAAAAATTAGATTTTT
TTGTGAATCAAATTTCAACAATCACACAACAATTTGGAAATTTAAAAAATCTGGCCCTTC
TTAATTTGTCTAAAAATCAACTTACAGAACTTTCTTCTGATGTTTTTATAAATTTAGTCA
ATCTTGAATATCTTTTACTCCATGATAATAATTTTACTTCACTGCCATTAGATATTTTTG
AAAGTCTTATTAACATTAAATCTTTGGCTCTTTTCAATAATAAGTTTACATCACTTCCTG
CAGGTATTTTTGATAATTTAGTTAAACTTGAAGTTCTCAGTTTAGGAGGAAACAGATTGA
CTTCACTTCCTTCTGAAATTTTTGATAATTTAACTAATCTTAGATATCTTGATCTTCCAA
ATAATCAATTGACAACACTTGATGAAAATTTTCTTAAAAATAATCATAAACTTGAAGAAA
TTAGGCTAAGTGGAAATAAAATCACAAAACTAAGTTACAAAATGTTTGAAAATAAAGAAG
ATTTAAAAAGAGTTTTTTTAGAAAGAAATGCATGCATCAATATTGATTTTTGGAGAACAT
TAACAATTGAAACAAGAAACGTCTTAAAAAATGAAATTTTAAATAATTGTTCATAA
>g17040.t12 Gene=g17040 Length=389
MAICFAFGSSELKCQLDYKLVDNNCIEKMNMIDGIITQEKCCTVTKCAIPDYKNGSYQQF
SVNEETKITENDAEIKPNYKSNKIEIFYIGKKCSGEKVDIFYLPIKVNEIFPNLISYTAY
RTKVKHLTKENFKGMKKLFYLGFVNNEIETIDDDTFDDLNELEYLNLESNKMKILNPRIF
MNNLKLEKLDFFVNQISTITQQFGNLKNLALLNLSKNQLTELSSDVFINLVNLEYLLLHD
NNFTSLPLDIFESLINIKSLALFNNKFTSLPAGIFDNLVKLEVLSLGGNRLTSLPSEIFD
NLTNLRYLDLPNNQLTTLDENFLKNNHKLEEIRLSGNKITKLSYKMFENKEDLKRVFLER
NACINIDFWRTLTIETRNVLKNEILNNCS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g17040.t12 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 9 | 389 | 0.000e+00 |
| 4 | g17040.t12 | PANTHER | PTHR45836:SF4 | PROTEIN SLIT | 126 | 267 | 0.000e+00 |
| 7 | g17040.t12 | PANTHER | PTHR45836 | SLIT HOMOLOG | 126 | 267 | 0.000e+00 |
| 5 | g17040.t12 | PANTHER | PTHR45836:SF4 | PROTEIN SLIT | 189 | 316 | 0.000e+00 |
| 8 | g17040.t12 | PANTHER | PTHR45836 | SLIT HOMOLOG | 189 | 316 | 0.000e+00 |
| 6 | g17040.t12 | PANTHER | PTHR45836:SF4 | PROTEIN SLIT | 245 | 364 | 0.000e+00 |
| 9 | g17040.t12 | PANTHER | PTHR45836 | SLIT HOMOLOG | 245 | 364 | 0.000e+00 |
| 2 | g17040.t12 | Pfam | PF13855 | Leucine rich repeat | 123 | 171 | 0.000e+00 |
| 3 | g17040.t12 | Pfam | PF13855 | Leucine rich repeat | 201 | 243 | 2.000e-07 |
| 1 | g17040.t12 | Pfam | PF13855 | Leucine rich repeat | 256 | 315 | 0.000e+00 |
| 25 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 137 | 158 | 5.494e+00 |
| 31 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 161 | 182 | 5.733e+00 |
| 33 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 185 | 207 | 5.694e+00 |
| 27 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 208 | 229 | 7.235e+00 |
| 32 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 232 | 253 | 7.211e+00 |
| 30 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 256 | 277 | 5.671e+00 |
| 29 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 280 | 301 | 7.750e+00 |
| 28 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 304 | 324 | 7.727e+00 |
| 26 | g17040.t12 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 328 | 349 | 6.719e+00 |
| 16 | g17040.t12 | SMART | SM00369 | LRR_typ_2 | 135 | 158 | 4.500e+01 |
| 21 | g17040.t12 | SMART | SM00365 | LRR_sd22_2 | 135 | 156 | 5.100e+02 |
| 12 | g17040.t12 | SMART | SM00369 | LRR_typ_2 | 159 | 182 | 9.000e+00 |
| 20 | g17040.t12 | SMART | SM00365 | LRR_sd22_2 | 183 | 208 | 5.300e+02 |
| 15 | g17040.t12 | SMART | SM00369 | LRR_typ_2 | 206 | 229 | 1.200e-01 |
| 11 | g17040.t12 | SMART | SM00369 | LRR_typ_2 | 230 | 253 | 5.500e-03 |
| 14 | g17040.t12 | SMART | SM00369 | LRR_typ_2 | 254 | 277 | 2.300e-01 |
| 17 | g17040.t12 | SMART | SM00369 | LRR_typ_2 | 278 | 301 | 1.700e-05 |
| 23 | g17040.t12 | SMART | SM00365 | LRR_sd22_2 | 278 | 301 | 1.300e+02 |
| 13 | g17040.t12 | SMART | SM00369 | LRR_typ_2 | 302 | 325 | 2.300e-01 |
| 22 | g17040.t12 | SMART | SM00365 | LRR_sd22_2 | 302 | 324 | 5.000e+01 |
| 19 | g17040.t12 | SMART | SM00365 | LRR_sd22_2 | 326 | 347 | 2.500e+01 |
| 18 | g17040.t12 | SMART | SM00369 | LRR_typ_2 | 327 | 349 | 3.600e+01 |
| 10 | g17040.t12 | SUPERFAMILY | SSF52058 | L domain-like | 99 | 363 | 0.000e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K16660 (reticulon-4 receptor-like 1)
Pathway
This gene does not belong to any 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