General information for g17040.t7
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.t7 | isoform | g17040.t7 | 12287237 | 12299240 |
| chr_4 | g17040 | g17040.t7 | exon | g17040.t7.exon1 | 12287237 | 12287673 |
| chr_4 | g17040 | g17040.t7 | exon | g17040.t7.exon2 | 12298042 | 12299240 |
| chr_4 | g17040 | g17040.t7 | cds | g17040.t7.CDS1 | 12298161 | 12299240 |
| chr_4 | g17040 | g17040.t7 | TSS | g17040.t7 | NA | NA |
| chr_4 | g17040 | g17040.t7 | TTS | g17040.t7 | NA | NA |
Sequences
>g17040.t7 Gene=g17040 Length=1636
TGTAAAAATATTTTTGTAAAAATTTGAACTAAATCTGAAAATTATTAAATATTTTTCTTT
AAAAGAGCACAGTTTGTTTTTCAATATTTTTTTATAAATAAATTTTGACCGAAAAAGGGT
AAAAGTCAATGTAACGAAAACTGTGTAGCACGTCACGCATTTATGAATTTTTTTTTTCGG
TTATCTTGAATGTTTACTAAATTAACTTTTTATTTCTTTTTCAGACCTTTGAAATGTTTT
TCATCAAATGTTTTTACTTTAACTGCGTGTTTATGGCGATTTGTTTTGCTTTTGGAAGCA
GTGAATTTAAATGTCAACTTGATTATAAACTTGTAGACAATAACTGCATCGAAAAAATGA
GTAGGTTTTTTTAAAAAAAAATATTTATTAAATTTTATTGAAAGGATGAAAACTTCTATA
GTTTTCATAAAATAAGCGCTATTTCATGCAAATTATTAAAAATGTTTATGAGATTTTAAT
AGTTTTTTGATAGATTTGAATCACCCCTTAATTTTATCTTTTACCCTAATTCATTTTATT
CATTTATATTTTAGACATGATTGATGGAATCATAACACAAGAAAAATGCTGTACGGTTAC
AAAATGTGCAATTCCTGATTATAAAAATGGAAGCTATCAACAATTTAGTGTCAACGAGGA
AACGAAAATTACTGAAAATGATGCAGAAATCAAACCTAACTATAAAAGCAATAAAATTGA
AATTTTTTATATTGGAAAAAAATGCAGTGGTGAAAAAGTTGACATTTTTTATCTTCCAAT
AAAAGTGAATGAAATTTTTCCAAATTTAATTTCTTACACTGCATATCGAACTAAAGTTAA
ACATTTGACAAAAGAAAATTTCAAAGGAATGAAAAAATTATTCTATTTAGGTTTTGTTAA
TAATGAAATTGAAACAATTGATGATGACACTTTTGATGATTTGAATGAGTTAGAATATTT
AAATTTGGAATCTAACAAAATGAAAATTTTAAATCCAAGAATTTTTATGAATAATCTAAA
ACTTGAAAAATTAGATTTTTTTGTGAATCAAATTTCAACAATCACACAACAATTTGGAAA
TTTAAAAAATCTGGCCCTTCTTAATTTGTCTAAAAATCAACTTACAGAACTTTCTTCTGA
TGTTTTTATAAATTTAGTCAATCTTGAATATCTTTTACTCCATGATAATAATTTTACTTC
ACTGCCATTAGATATTTTTGAAAGTCTTATTAACATTAAATCTTTGGCTCTTTTCAATAA
TAAGTTTACATCACTTCCTGCAGGTATTTTTGATAATTTAGTTAAACTTGAAGTTCTCAG
TTTAGGAGGAAACAGATTGACTTCACTTCCTTCTGAAATTTTTGATAATTTAACTAATCT
TAGATATCTTGATCTTCCAAATAATCAATTGACAACACTTGATGAAAATTTTCTTAAAAA
TAATCATAAACTTGAAGAAATTAGGCTAAGTGGAAATAAAATCACAAAACTAAGTTACAA
AATGTTTGAAAATAAAGAAGATTTAAAAAGAGTTTTTTTAGAAAGAAATGCATGCATCAA
TATTGATTTTTGGAGAACATTAACAATTGAAACAAGAAACGTCTTAAAAAATGAAATTTT
AAATAATTGTTCATAA
>g17040.t7 Gene=g17040 Length=359
MIDGIITQEKCCTVTKCAIPDYKNGSYQQFSVNEETKITENDAEIKPNYKSNKIEIFYIG
KKCSGEKVDIFYLPIKVNEIFPNLISYTAYRTKVKHLTKENFKGMKKLFYLGFVNNEIET
IDDDTFDDLNELEYLNLESNKMKILNPRIFMNNLKLEKLDFFVNQISTITQQFGNLKNLA
LLNLSKNQLTELSSDVFINLVNLEYLLLHDNNFTSLPLDIFESLINIKSLALFNNKFTSL
PAGIFDNLVKLEVLSLGGNRLTSLPSEIFDNLTNLRYLDLPNNQLTTLDENFLKNNHKLE
EIRLSGNKITKLSYKMFENKEDLKRVFLERNACINIDFWRTLTIETRNVLKNEILNNCS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g17040.t7 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 62 | 202 | 0.000e+00 |
| 24 | g17040.t7 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 203 | 358 | 0.000e+00 |
| 4 | g17040.t7 | PANTHER | PTHR45712 | AGAP008170-PA | 94 | 291 | 0.000e+00 |
| 6 | g17040.t7 | PANTHER | PTHR45712:SF22 | AGAP008170-PA | 94 | 291 | 0.000e+00 |
| 5 | g17040.t7 | PANTHER | PTHR45712 | AGAP008170-PA | 158 | 337 | 0.000e+00 |
| 7 | g17040.t7 | PANTHER | PTHR45712:SF22 | AGAP008170-PA | 158 | 337 | 0.000e+00 |
| 9 | g17040.t7 | PRINTS | PR00019 | Leucine-rich repeat signature | 179 | 192 | 9.300e-05 |
| 8 | g17040.t7 | PRINTS | PR00019 | Leucine-rich repeat signature | 272 | 285 | 9.300e-05 |
| 2 | g17040.t7 | Pfam | PF13855 | Leucine rich repeat | 93 | 141 | 0.000e+00 |
| 3 | g17040.t7 | Pfam | PF13855 | Leucine rich repeat | 164 | 213 | 2.000e-07 |
| 1 | g17040.t7 | Pfam | PF13855 | Leucine rich repeat | 226 | 285 | 0.000e+00 |
| 31 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 107 | 128 | 5.494e+00 |
| 33 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 131 | 152 | 5.733e+00 |
| 34 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 155 | 177 | 5.694e+00 |
| 26 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 178 | 199 | 7.235e+00 |
| 27 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 202 | 223 | 7.211e+00 |
| 29 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 226 | 247 | 5.671e+00 |
| 32 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 250 | 271 | 7.750e+00 |
| 30 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 274 | 294 | 7.727e+00 |
| 28 | g17040.t7 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 298 | 319 | 6.719e+00 |
| 12 | g17040.t7 | SMART | SM00369 | LRR_typ_2 | 105 | 128 | 4.500e+01 |
| 21 | g17040.t7 | SMART | SM00365 | LRR_sd22_2 | 105 | 126 | 5.100e+02 |
| 17 | g17040.t7 | SMART | SM00369 | LRR_typ_2 | 129 | 152 | 9.000e+00 |
| 23 | g17040.t7 | SMART | SM00365 | LRR_sd22_2 | 153 | 178 | 5.300e+02 |
| 13 | g17040.t7 | SMART | SM00369 | LRR_typ_2 | 176 | 199 | 1.200e-01 |
| 16 | g17040.t7 | SMART | SM00369 | LRR_typ_2 | 200 | 223 | 5.500e-03 |
| 14 | g17040.t7 | SMART | SM00369 | LRR_typ_2 | 224 | 247 | 2.300e-01 |
| 15 | g17040.t7 | SMART | SM00369 | LRR_typ_2 | 248 | 271 | 1.700e-05 |
| 20 | g17040.t7 | SMART | SM00365 | LRR_sd22_2 | 248 | 271 | 1.300e+02 |
| 11 | g17040.t7 | SMART | SM00369 | LRR_typ_2 | 272 | 295 | 2.300e-01 |
| 22 | g17040.t7 | SMART | SM00365 | LRR_sd22_2 | 272 | 294 | 5.000e+01 |
| 19 | g17040.t7 | SMART | SM00365 | LRR_sd22_2 | 296 | 317 | 2.500e+01 |
| 18 | g17040.t7 | SMART | SM00369 | LRR_typ_2 | 297 | 319 | 3.600e+01 |
| 10 | g17040.t7 | SUPERFAMILY | SSF52058 | L domain-like | 69 | 333 | 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