General information for g17040.t1
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.t1 | TSS | g17040.t1 | 12287456 | 12287456 |
| chr_4 | g17040 | g17040.t1 | isoform | g17040.t1 | 12297939 | 12299240 |
| chr_4 | g17040 | g17040.t1 | exon | g17040.t1.exon1 | 12297939 | 12297942 |
| chr_4 | g17040 | g17040.t1 | cds | g17040.t1.CDS1 | 12297939 | 12297942 |
| chr_4 | g17040 | g17040.t1 | exon | g17040.t1.exon2 | 12298159 | 12299240 |
| chr_4 | g17040 | g17040.t1 | cds | g17040.t1.CDS2 | 12298159 | 12299240 |
| chr_4 | g17040 | g17040.t1 | TTS | g17040.t1 | NA | NA |
Sequences
>g17040.t1 Gene=g17040 Length=1086
ATGAACATGATTGATGGAATCATAACACAAGAAAAATGCTGTACGGTTACAAAATGTGCA
ATTCCTGATTATAAAAATGGAAGCTATCAACAATTTAGTGTCAACGAGGAAACGAAAATT
ACTGAAAATGATGCAGAAATCAAACCTAACTATAAAAGCAATAAAATTGAAATTTTTTAT
ATTGGAAAAAAATGCAGTGGTGAAAAAGTTGACATTTTTTATCTTCCAATAAAAGTGAAT
GAAATTTTTCCAAATTTAATTTCTTACACTGCATATCGAACTAAAGTTAAACATTTGACA
AAAGAAAATTTCAAAGGAATGAAAAAATTATTCTATTTAGGTTTTGTTAATAATGAAATT
GAAACAATTGATGATGACACTTTTGATGATTTGAATGAGTTAGAATATTTAAATTTGGAA
TCTAACAAAATGAAAATTTTAAATCCAAGAATTTTTATGAATAATCTAAAACTTGAAAAA
TTAGATTTTTTTGTGAATCAAATTTCAACAATCACACAACAATTTGGAAATTTAAAAAAT
CTGGCCCTTCTTAATTTGTCTAAAAATCAACTTACAGAACTTTCTTCTGATGTTTTTATA
AATTTAGTCAATCTTGAATATCTTTTACTCCATGATAATAATTTTACTTCACTGCCATTA
GATATTTTTGAAAGTCTTATTAACATTAAATCTTTGGCTCTTTTCAATAATAAGTTTACA
TCACTTCCTGCAGGTATTTTTGATAATTTAGTTAAACTTGAAGTTCTCAGTTTAGGAGGA
AACAGATTGACTTCACTTCCTTCTGAAATTTTTGATAATTTAACTAATCTTAGATATCTT
GATCTTCCAAATAATCAATTGACAACACTTGATGAAAATTTTCTTAAAAATAATCATAAA
CTTGAAGAAATTAGGCTAAGTGGAAATAAAATCACAAAACTAAGTTACAAAATGTTTGAA
AATAAAGAAGATTTAAAAAGAGTTTTTTTAGAAAGAAATGCATGCATCAATATTGATTTT
TGGAGAACATTAACAATTGAAACAAGAAACGTCTTAAAAAATGAAATTTTAAATAATTGT
TCATAA
>g17040.t1 Gene=g17040 Length=361
MNMIDGIITQEKCCTVTKCAIPDYKNGSYQQFSVNEETKITENDAEIKPNYKSNKIEIFY
IGKKCSGEKVDIFYLPIKVNEIFPNLISYTAYRTKVKHLTKENFKGMKKLFYLGFVNNEI
ETIDDDTFDDLNELEYLNLESNKMKILNPRIFMNNLKLEKLDFFVNQISTITQQFGNLKN
LALLNLSKNQLTELSSDVFINLVNLEYLLLHDNNFTSLPLDIFESLINIKSLALFNNKFT
SLPAGIFDNLVKLEVLSLGGNRLTSLPSEIFDNLTNLRYLDLPNNQLTTLDENFLKNNHK
LEEIRLSGNKITKLSYKMFENKEDLKRVFLERNACINIDFWRTLTIETRNVLKNEILNNC
S
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 27 | g17040.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 64 | 204 | 0.000e+00 |
| 26 | g17040.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 205 | 360 | 0.000e+00 |
| 4 | g17040.t1 | PANTHER | PTHR45836:SF4 | PROTEIN SLIT | 96 | 239 | 0.000e+00 |
| 7 | g17040.t1 | PANTHER | PTHR45836 | SLIT HOMOLOG | 96 | 239 | 0.000e+00 |
| 6 | g17040.t1 | PANTHER | PTHR45836:SF4 | PROTEIN SLIT | 163 | 288 | 0.000e+00 |
| 9 | g17040.t1 | PANTHER | PTHR45836 | SLIT HOMOLOG | 163 | 288 | 0.000e+00 |
| 5 | g17040.t1 | PANTHER | PTHR45836:SF4 | PROTEIN SLIT | 209 | 336 | 0.000e+00 |
| 8 | g17040.t1 | PANTHER | PTHR45836 | SLIT HOMOLOG | 209 | 336 | 0.000e+00 |
| 11 | g17040.t1 | PRINTS | PR00019 | Leucine-rich repeat signature | 181 | 194 | 9.400e-05 |
| 10 | g17040.t1 | PRINTS | PR00019 | Leucine-rich repeat signature | 274 | 287 | 9.400e-05 |
| 1 | g17040.t1 | Pfam | PF13855 | Leucine rich repeat | 95 | 143 | 0.000e+00 |
| 3 | g17040.t1 | Pfam | PF13855 | Leucine rich repeat | 166 | 215 | 2.000e-07 |
| 2 | g17040.t1 | Pfam | PF13855 | Leucine rich repeat | 228 | 287 | 0.000e+00 |
| 31 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 109 | 130 | 5.494e+00 |
| 29 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 133 | 154 | 5.733e+00 |
| 35 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 157 | 179 | 5.694e+00 |
| 28 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 180 | 201 | 7.235e+00 |
| 33 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 204 | 225 | 7.211e+00 |
| 30 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 228 | 249 | 5.671e+00 |
| 34 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 252 | 273 | 7.750e+00 |
| 36 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 276 | 296 | 7.727e+00 |
| 32 | g17040.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 300 | 321 | 6.719e+00 |
| 14 | g17040.t1 | SMART | SM00369 | LRR_typ_2 | 107 | 130 | 4.500e+01 |
| 23 | g17040.t1 | SMART | SM00365 | LRR_sd22_2 | 107 | 128 | 5.100e+02 |
| 17 | g17040.t1 | SMART | SM00369 | LRR_typ_2 | 131 | 154 | 9.000e+00 |
| 22 | g17040.t1 | SMART | SM00365 | LRR_sd22_2 | 155 | 180 | 5.300e+02 |
| 20 | g17040.t1 | SMART | SM00369 | LRR_typ_2 | 178 | 201 | 1.200e-01 |
| 16 | g17040.t1 | SMART | SM00369 | LRR_typ_2 | 202 | 225 | 5.500e-03 |
| 19 | g17040.t1 | SMART | SM00369 | LRR_typ_2 | 226 | 249 | 2.300e-01 |
| 18 | g17040.t1 | SMART | SM00369 | LRR_typ_2 | 250 | 273 | 1.700e-05 |
| 21 | g17040.t1 | SMART | SM00365 | LRR_sd22_2 | 250 | 273 | 1.300e+02 |
| 15 | g17040.t1 | SMART | SM00369 | LRR_typ_2 | 274 | 297 | 2.300e-01 |
| 25 | g17040.t1 | SMART | SM00365 | LRR_sd22_2 | 274 | 296 | 5.000e+01 |
| 24 | g17040.t1 | SMART | SM00365 | LRR_sd22_2 | 298 | 319 | 2.500e+01 |
| 13 | g17040.t1 | SMART | SM00369 | LRR_typ_2 | 299 | 321 | 3.600e+01 |
| 12 | g17040.t1 | SUPERFAMILY | SSF52058 | L domain-like | 71 | 335 | 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