Gene loci information

Transcript annotation

  • This transcript has been annotated as Argininosuccinate lyase.

Parent gene

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 g4422 g4422.t1 isoform g4422.t1 2110205 2111667
chr_2 g4422 g4422.t1 exon g4422.t1.exon1 2110205 2111116
chr_2 g4422 g4422.t1 cds g4422.t1.CDS1 2110205 2111116
chr_2 g4422 g4422.t1 exon g4422.t1.exon2 2111176 2111667
chr_2 g4422 g4422.t1 cds g4422.t1.CDS2 2111176 2111667
chr_2 g4422 g4422.t1 TSS g4422.t1 2111732 2111732
chr_2 g4422 g4422.t1 TTS g4422.t1 NA NA

Sequences

>g4422.t1 Gene=g4422 Length=1404
ATGGAGCAAAAAACGTCAAAATTATGGGGCTGTGATGGACGATTTGCTCGTCAAATGAAT
GATAATTTAGCACAATTAAACAACTCACTCCACATTGATAAACGACTTGTTCAAGAAGAC
ATTTTCGGCAGTTTTGCGTATTCGAAAAGTTTATGTCAAGCTCAAATCATTCAGCCGAAT
GAGCTGGAAATGATCCAAAGTGCGTTATATGAAATTAGTAATGAATGGAAAAATGGTACA
GTAGTTTTGAAGGATGATGATGAAGATATTCACAGTGCAAATGAACGGCTTTTAATTGAG
AAAATTGGCAATGTTGGAAGAAAAATTCACACTGGCAGAAGTAGAAATGATCAAGTAATT
CTTGACATGAAATTATGGATAAAAAAAGCAATATCAGATATTCTTGAAATTTTTTCAACT
TTTTTGAATGTTATAATAGAAAAAGCTGAAGAGAATATTGATATTTTGATGCCTGGTTAT
ACACATTTACAAAGAGCACAACCAATTCGCGTTAGTCATTGGCTTCTTTCATATGGATTC
TTTTTTCAAGCTGATTGTGAAAGATTAAAGCAAATATTTGAGAGAGTCAATTTGAGTATG
CCACTTGGTTCTGGTGCTATCAGTGGAAATCCTTTTGAAATTGATCGTATTGAATTGGCA
AAAAATTTGAACTTTAGAGGAGTTACAATGAATTCAATGAATGCTGTTAGTGATCGAGAT
TTTGTTTGTGAATTTAATTTTGTTGCTTCAATGATTTCAATACACTTGAGTCGTTTATCA
GAAGATTTAATTTTATATAGCACAAAAGAGTTTAATTATATAAAATTATCAAATGAATTT
TGTACTGGTTCCAGTTTAATGCCACAAAAATTTAATGCTGACAGCATTGAGTTAGTTAGA
GGAACTACTGGAAGTATAATTGGTCAATTGATGAATATATTAACAACTTTAAAAGGATTA
CCATCAACTTATAATAAAGATTTGCAGGGAGACAAAGAATCAATGTTTTATGTTTATGAC
AAGATAATTTTATCACTAAAAGTCATGGTTGGTGTCATTGATACTTTGGAAATTTTTAAA
GAAAATTGTTGGAATGCTCTTAGTTATGACATGCTAGCAACTGATTTAGCATATTATTTG
GTACGTAAAGGTAAAGCATTTAGAGATGCTCATCATTGTGCTTCAGCTGTTGTTGATGTT
GCTTCAAAAAGCGGTGTTGATATTAACAAATTGCCTCTGACTGCATTCAAAATGGTAAGC
GAAAGTTTCAATGAAGATGTCTATAATATTTTCAGTTTTGAAAAAAGTGTTGAACAATAT
CAAATTATTGGTGGTACTAGCAAGACATCTGTCTTGGAACAAATTGCGCATTTGAAAGAG
TTTGCTGCAAATTTGAAATGTTAA

>g4422.t1 Gene=g4422 Length=467
MEQKTSKLWGCDGRFARQMNDNLAQLNNSLHIDKRLVQEDIFGSFAYSKSLCQAQIIQPN
ELEMIQSALYEISNEWKNGTVVLKDDDEDIHSANERLLIEKIGNVGRKIHTGRSRNDQVI
LDMKLWIKKAISDILEIFSTFLNVIIEKAEENIDILMPGYTHLQRAQPIRVSHWLLSYGF
FFQADCERLKQIFERVNLSMPLGSGAISGNPFEIDRIELAKNLNFRGVTMNSMNAVSDRD
FVCEFNFVASMISIHLSRLSEDLILYSTKEFNYIKLSNEFCTGSSLMPQKFNADSIELVR
GTTGSIIGQLMNILTTLKGLPSTYNKDLQGDKESMFYVYDKIILSLKVMVGVIDTLEIFK
ENCWNALSYDMLATDLAYYLVRKGKAFRDAHHCASAVVDVASKSGVDINKLPLTAFKMVS
ESFNEDVYNIFSFEKSVEQYQIIGGTSKTSVLEQIAHLKEFAANLKC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g4422.t1 CDD cd01359 Argininosuccinate_lyase 29 461 0.0
17 g4422.t1 Gene3D G3DSA:1.10.275.10 - 32 237 5.8E-169
19 g4422.t1 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain) 126 455 5.8E-169
18 g4422.t1 Gene3D G3DSA:1.10.40.30 - 368 439 5.8E-169
5 g4422.t1 Hamap MF_00006 Argininosuccinate lyase [argH]. 7 460 35.255314
3 g4422.t1 PANTHER PTHR43814:SF1 ARGININOSUCCINATE LYASE 3 461 1.9E-168
4 g4422.t1 PANTHER PTHR43814 ARGININOSUCCINATE LYASE 3 461 1.9E-168
11 g4422.t1 PRINTS PR00145 Argininosuccinate lyase family signature 108 130 4.0E-55
13 g4422.t1 PRINTS PR00149 Fumarate lyase superfamily signature 109 127 6.7E-24
9 g4422.t1 PRINTS PR00145 Argininosuccinate lyase family signature 149 169 4.0E-55
12 g4422.t1 PRINTS PR00149 Fumarate lyase superfamily signature 154 172 6.7E-24
8 g4422.t1 PRINTS PR00145 Argininosuccinate lyase family signature 201 217 4.0E-55
10 g4422.t1 PRINTS PR00145 Argininosuccinate lyase family signature 239 263 4.0E-55
15 g4422.t1 PRINTS PR00149 Fumarate lyase superfamily signature 239 266 6.7E-24
7 g4422.t1 PRINTS PR00145 Argininosuccinate lyase family signature 283 299 4.0E-55
14 g4422.t1 PRINTS PR00149 Fumarate lyase superfamily signature 283 299 6.7E-24
6 g4422.t1 PRINTS PR00145 Argininosuccinate lyase family signature 318 337 4.0E-55
1 g4422.t1 Pfam PF00206 Lyase 14 308 3.8E-73
2 g4422.t1 Pfam PF14698 Argininosuccinate lyase C-terminal 371 438 3.4E-17
21 g4422.t1 ProSitePatterns PS00163 Fumarate lyases signature. 283 292 -
16 g4422.t1 SUPERFAMILY SSF48557 L-aspartase-like 13 463 2.2E-118
22 g4422.t1 TIGRFAM TIGR00838 argH: argininosuccinate lyase 12 460 1.7E-162

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:0004056 argininosuccinate lyase activity MF
GO:0042450 arginine biosynthetic process via ornithine BP
GO:0003824 catalytic activity MF

KEGG

Orthology

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