General information for g13250.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CAD protein.
Parent gene
- The parent gene g13250 is located on chr_1: 28782803..28785813 (- 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_1 | g13250 | g13250.t1 | isoform | g13250.t1 | 28782803 | 28785813 |
| chr_1 | g13250 | g13250.t1 | exon | g13250.t1.exon1 | 28782803 | 28785209 |
| chr_1 | g13250 | g13250.t1 | cds | g13250.t1.CDS1 | 28782803 | 28785209 |
| chr_1 | g13250 | g13250.t1 | exon | g13250.t1.exon2 | 28785274 | 28785407 |
| chr_1 | g13250 | g13250.t1 | cds | g13250.t1.CDS2 | 28785274 | 28785407 |
| chr_1 | g13250 | g13250.t1 | exon | g13250.t1.exon3 | 28785763 | 28785813 |
| chr_1 | g13250 | g13250.t1 | cds | g13250.t1.CDS3 | 28785763 | 28785813 |
| chr_1 | g13250 | g13250.t1 | TSS | g13250.t1 | NA | NA |
| chr_1 | g13250 | g13250.t1 | TTS | g13250.t1 | NA | NA |
Sequences
>g13250.t1 Gene=g13250 Length=2592
ATGAAAAGCACCGAGAGAACTGACAAAAACTTAATTGAAATTATTTGTAGAGTTGAAGCT
GTTCAATGGACATTTGATGAAATCAATAGTGAGAGTGGCGAACTTCATCATTTGGCAGCA
TTTTTAGCTGATAAAAAAATTGAGCTTGTTATTTGCTTGCCAATGAGAGGAGGCGGTGCT
AGAAGAGTTTCCTCATTCATGACTCATGGATATAGAACTCGACGACTTGCCGTTGATTAC
TCAATTCCACTCGTGACTGATGTCAAATGTACGAAATTACTTGTCGAAGCTATGAGACTT
TCGGGACGTGCTCCACCGATGAAAACACATACTGATTGCATGACCAGTCGCCAAATGATC
AAACTTCCTGGTTTTATTGACGTTCATGTTCATTTACGTGAACCAGGTGCAACACATAAA
GAAGATTTTGCTTCAGGAACAGCTGCAGCTCTTGCTGGTGGCATAACACTTGTCTGTGCA
ATGCCAAACACAAATCCAGCTATTGTCAACCAACAAAACTTTTCACTTTTCAAAGAATGT
GCGAAGAATGGTGCACGTTGTGATTATGCATTGTTTGTTGGCGCATCATCAGACAATTAT
CATCAAATTTGTGAACTTGCTCCAGAAGCGGCAGCCTTGAAAATGTACTTAAATGAAACA
TTCACTACATTGAAACTCAATGACATGACAGTGTGGGAAAAGCATCTGAGTAATTGGCCA
AAACACGCTCCGTTGTGTGTGCATGCTGAAAAACAAGCAACTGCTGCAATTATTTTACTC
GCAAATCTTATCGATCGTCCAATTCACGTGTGTCATGTTGCAAGAAAAGAAGAAATTCAA
ATTATTAAAACAGCAAAGGAACGCGGCATGAAAATTACTTGTGAAGTTTGCCCTCATCAT
TTATTTTTGTCAACAAAAGATCTAAGTCGTATTGGTTATGGTCGTGGTGAAGTTCGTCCA
ATTTTATGCTCTCCTGAAGATCAACAAGCATTGTGGGATAATATGGATATTATTGATTGC
TTTGCTACTGATCATGCACCACATACAATTGAAGAAAAAGATTCAGAAAAACCACCACCT
GGTTTTCCAGGTCTCGAGACAATTTTGCCTCTGCTTTTGACTGCTGTCAATGATGGTCGC
TTAACAATGGATGATTTAATTAACAAATTTTACAAAAATCCAAGAAAAATTTTCAGTTTA
CCAGAACAACACAATACTTATGTTGAAGTGGATATGGATGAAGAATGGATTATTCCTAAT
GTATTGACTCATTCCAAAGCAAAATGGACACCATTTGCTGGAATGAAAGTCAAAGGTTGT
GTCTCACGAGTCGTTTTGCGAGGTGAAGTTGCATTTGTCGATGGAGAAGTTCTTGTTGAG
CCTGGGTTTGGTCAAAATGTTCGTCAGTGGAGAACTCGAATGACAGATGAAGAAAGATTA
TCATTAGGATCTTGTGAAAAAATCAATGCTTCATTTGAACATTTAGATGAAGAACTACAA
GTTAAAATTCCTGATGCAGCAACATCAAAACTACCAAGTTATTATTCTGCATTGTCACCA
TTACCACGCACTCGTTTGGATTCAGCTGGAAGTCAACTTTATAAAGATTATATTCCAGAA
TCATTTGGTCGCTCTTTCTCAAAAAATATGAATGGAAAACATATTTTAAGCGTTGACATG
TTCACTTCAAAAGATCAATTGAGAGATATTTTCGACCTTGCAAAAACATTTAAAGCAAGT
GTACAAAAGAAAGGTTGGTTTGATGAAGTTTTGCGTGGAAAAGTTATGGCTTCATGTTTC
TATGAAGTTTCGACTAGAACTTGTTGTAGTTTTGCTGCTGCAATGCAAAGACTTGGTGGA
CGAGTTATTTACATGGATGAAACAAGCTCATCTGTTAAGAAAGGAGAAACACTTGAAGAT
TCAATTGCTGTAATGTCAGGTTATGCTGACGTTGTAGTTTTACGTCATCCAGAGGTTGGT
GCTATGGCACGAGCAGCTGATGTGTCACAAAAACCTGTTATCAATGCTGGTGATGGAATT
GGCGAACATCCTACTCAAGCACTTCTTGATGTTTTTACTATTCGTGAAGAATTTGGTACA
GTTAAAGGCTTAACAATTACAATGGTTGGTGATTTAAAACATGGAAGAACAGTTCATTCA
TTAGCTCGTTTGCTAACTCTTTACGATGTGTCAATCAATTACGTTTCTCCAGCATCATTA
GCAATGCCCGAAAAAGTCATCAAATTCGTGGCCTCAAAGGGAATTTCACAGCATTTTTAC
ACTTCACTTGACGAGATTTTACCTGAGACAGATGTACTTTATATGACTCGTATTCAAAAG
GAACGCTTTTCAAATGAAGAAGAATATAAAAGTACTTGCGGTTTGTATGTTGTTACTCCT
AAATTAATGACACGTGCAAAACCTAAGATGATTGTCATGCATCCATTACCGAGAAATGAT
GAAATTGACAAGGCATTTGACAATGACAAACGTGCAGCTTACTTTAGACAGGCTGAATAT
GGAATGTATGTTCGCATGAGTATTCTTGCTATGGTTCTAGGCTTTGAAGGTTTTAAGGCT
ACAAGAAAATGA
>g13250.t1 Gene=g13250 Length=863
MKSTERTDKNLIEIICRVEAVQWTFDEINSESGELHHLAAFLADKKIELVICLPMRGGGA
RRVSSFMTHGYRTRRLAVDYSIPLVTDVKCTKLLVEAMRLSGRAPPMKTHTDCMTSRQMI
KLPGFIDVHVHLREPGATHKEDFASGTAAALAGGITLVCAMPNTNPAIVNQQNFSLFKEC
AKNGARCDYALFVGASSDNYHQICELAPEAAALKMYLNETFTTLKLNDMTVWEKHLSNWP
KHAPLCVHAEKQATAAIILLANLIDRPIHVCHVARKEEIQIIKTAKERGMKITCEVCPHH
LFLSTKDLSRIGYGRGEVRPILCSPEDQQALWDNMDIIDCFATDHAPHTIEEKDSEKPPP
GFPGLETILPLLLTAVNDGRLTMDDLINKFYKNPRKIFSLPEQHNTYVEVDMDEEWIIPN
VLTHSKAKWTPFAGMKVKGCVSRVVLRGEVAFVDGEVLVEPGFGQNVRQWRTRMTDEERL
SLGSCEKINASFEHLDEELQVKIPDAATSKLPSYYSALSPLPRTRLDSAGSQLYKDYIPE
SFGRSFSKNMNGKHILSVDMFTSKDQLRDIFDLAKTFKASVQKKGWFDEVLRGKVMASCF
YEVSTRTCCSFAAAMQRLGGRVIYMDETSSSVKKGETLEDSIAVMSGYADVVVLRHPEVG
AMARAADVSQKPVINAGDGIGEHPTQALLDVFTIREEFGTVKGLTITMVGDLKHGRTVHS
LARLLTLYDVSINYVSPASLAMPEKVIKFVASKGISQHFYTSLDEILPETDVLYMTRIQK
ERFSNEEEYKSTCGLYVVTPKLMTRAKPKMIVMHPLPRNDEIDKAFDNDKRAAYFRQAEY
GMYVRMSILAMVLGFEGFKATRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 29 | g13250.t1 | CDD | cd01316 | CAD_DHOase | 118 | 464 | 0.0 |
| 22 | g13250.t1 | Gene3D | G3DSA:3.40.50.1380 | - | 1 | 99 | 1.8E-18 |
| 25 | g13250.t1 | Gene3D | G3DSA:3.20.20.140 | - | 112 | 479 | 2.3E-152 |
| 24 | g13250.t1 | Gene3D | G3DSA:3.40.50.1370 | - | 554 | 851 | 1.2E-118 |
| 23 | g13250.t1 | Gene3D | G3DSA:3.40.50.1370 | - | 683 | 840 | 1.2E-118 |
| 7 | g13250.t1 | Hamap | MF_00001 | Aspartate carbamoyltransferase [pyrB]. | 552 | 855 | 33.844242 |
| 5 | g13250.t1 | PANTHER | PTHR43668 | ALLANTOINASE | 48 | 465 | 1.0E-137 |
| 6 | g13250.t1 | PANTHER | PTHR43668:SF4 | DIHYDROOROTASE | 48 | 465 | 1.0E-137 |
| 17 | g13250.t1 | PRINTS | PR00101 | Aspartate carbamoyltransferase signature | 590 | 612 | 5.6E-36 |
| 11 | g13250.t1 | PRINTS | PR00100 | Aspartate/ornithine carbamoyltransferase superfamily signature | 600 | 619 | 1.2E-19 |
| 15 | g13250.t1 | PRINTS | PR00101 | Aspartate carbamoyltransferase signature | 628 | 637 | 5.6E-36 |
| 14 | g13250.t1 | PRINTS | PR00101 | Aspartate carbamoyltransferase signature | 682 | 699 | 5.6E-36 |
| 8 | g13250.t1 | PRINTS | PR00100 | Aspartate/ornithine carbamoyltransferase superfamily signature | 683 | 694 | 1.2E-19 |
| 16 | g13250.t1 | PRINTS | PR00101 | Aspartate carbamoyltransferase signature | 773 | 782 | 5.6E-36 |
| 10 | g13250.t1 | PRINTS | PR00100 | Aspartate/ornithine carbamoyltransferase superfamily signature | 808 | 817 | 1.2E-19 |
| 13 | g13250.t1 | PRINTS | PR00101 | Aspartate carbamoyltransferase signature | 812 | 817 | 5.6E-36 |
| 9 | g13250.t1 | PRINTS | PR00100 | Aspartate/ornithine carbamoyltransferase superfamily signature | 818 | 841 | 1.2E-19 |
| 12 | g13250.t1 | PRINTS | PR00101 | Aspartate carbamoyltransferase signature | 834 | 848 | 5.6E-36 |
| 1 | g13250.t1 | Pfam | PF02142 | MGS-like domain | 3 | 86 | 3.0E-6 |
| 3 | g13250.t1 | Pfam | PF01979 | Amidohydrolase family | 121 | 346 | 4.6E-11 |
| 2 | g13250.t1 | Pfam | PF02729 | Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain | 553 | 696 | 7.5E-43 |
| 4 | g13250.t1 | Pfam | PF00185 | Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain | 702 | 851 | 4.7E-34 |
| 27 | g13250.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 839 | - |
| 28 | g13250.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 840 | 858 | - |
| 26 | g13250.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 859 | 863 | - |
| 31 | g13250.t1 | ProSitePatterns | PS00482 | Dihydroorotase signature 1. | 127 | 135 | - |
| 30 | g13250.t1 | ProSitePatterns | PS00483 | Dihydroorotase signature 2. | 342 | 353 | - |
| 32 | g13250.t1 | ProSitePatterns | PS00097 | Aspartate and ornithine carbamoyltransferases signature. | 600 | 607 | - |
| 34 | g13250.t1 | ProSiteProfiles | PS51855 | MGS-like domain profile. | 1 | 120 | 10.266 |
| 18 | g13250.t1 | SUPERFAMILY | SSF52335 | Methylglyoxal synthase-like | 3 | 127 | 3.66E-12 |
| 20 | g13250.t1 | SUPERFAMILY | SSF51556 | Metallo-dependent hydrolases | 124 | 403 | 5.33E-81 |
| 21 | g13250.t1 | SUPERFAMILY | SSF51338 | Composite domain of metallo-dependent hydrolases | 357 | 472 | 1.04E-18 |
| 19 | g13250.t1 | SUPERFAMILY | SSF53671 | Aspartate/ornithine carbamoyltransferase | 549 | 854 | 2.36E-98 |
| 33 | g13250.t1 | TIGRFAM | TIGR00670 | asp_carb_tr: aspartate carbamoyltransferase | 553 | 853 | 4.9E-104 |
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:0016743 | carboxyl- or carbamoyltransferase activity | MF |
| GO:0016597 | amino acid binding | MF |
| GO:0006520 | cellular amino acid metabolic process | BP |
| GO:0004070 | aspartate carbamoyltransferase activity | MF |
| GO:0016812 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides | MF |
| GO:0016787 | hydrolase activity | MF |
| GO:0006207 | ‘de novo’ pyrimidine nucleobase biosynthetic process | BP |
| GO:0016810 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds | MF |
KEGG
Orthology
- This transcript has been annotated with K00609 (aspartate carbamoyltransferase catalytic subunit)
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.
