General information for g8427.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CTL-like protein 1.
Parent gene
- The parent gene g8427 is located on chr_2: 30412119..30413248 (+ 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_2 | g8427 | g8427.t1 | TSS | g8427.t1 | 30409777 | 30409777 |
| chr_2 | g8427 | g8427.t1 | isoform | g8427.t1 | 30410014 | 30412651 |
| chr_2 | g8427 | g8427.t1 | exon | g8427.t1.exon1 | 30410014 | 30410118 |
| chr_2 | g8427 | g8427.t1 | cds | g8427.t1.CDS1 | 30410014 | 30410118 |
| chr_2 | g8427 | g8427.t1 | exon | g8427.t1.exon2 | 30410473 | 30411245 |
| chr_2 | g8427 | g8427.t1 | cds | g8427.t1.CDS2 | 30410473 | 30411245 |
| chr_2 | g8427 | g8427.t1 | exon | g8427.t1.exon3 | 30411304 | 30411723 |
| chr_2 | g8427 | g8427.t1 | cds | g8427.t1.CDS3 | 30411304 | 30411723 |
| chr_2 | g8427 | g8427.t1 | exon | g8427.t1.exon4 | 30411789 | 30412050 |
| chr_2 | g8427 | g8427.t1 | cds | g8427.t1.CDS4 | 30411789 | 30412050 |
| chr_2 | g8427 | g8427.t1 | exon | g8427.t1.exon5 | 30412115 | 30412426 |
| chr_2 | g8427 | g8427.t1 | cds | g8427.t1.CDS5 | 30412115 | 30412426 |
| chr_2 | g8427 | g8427.t1 | exon | g8427.t1.exon6 | 30412484 | 30412651 |
| chr_2 | g8427 | g8427.t1 | cds | g8427.t1.CDS6 | 30412484 | 30412651 |
| chr_2 | g8427 | g8427.t1 | TTS | g8427.t1 | 30413247 | 30413247 |
Sequences
>g8427.t1 Gene=g8427 Length=2040
ATGGGTTGTTTTGAGTCTAAACAGAACCGTACTGATCCAGTTGCGGTTAGAGGTTGTACA
GATGTATGCTGGCTAGTAATTTTCATTCTTTTTTGGGTTTTATTGATCGTTATTGCTGCT
TTTGCTTTTGTATATGGAAATCCACAACGCATAATCAACGGCTATGATTCATTCGGTAAT
ACGTGTGGTGTTTCTGATAATAAAAATTATGCAGACATCTCTTATGGAAAGGCAGCCGGT
ATTGATACAAGTGATAAGAAGTTTGTTTATTTCTTCAACATAAAGGAAATTAAAAAGTCA
TTAAAAATTTGTGTAAAACAATGCCCATCAAAACAGCTAAATACTTCCGTTCAATTATAT
GATTATTATAGAGAAAAGGATACAAGCTATTGTCGATATGATTTTGATATGAACAAATTG
ACTAGAGCAAGTGATAATGATGAGTTAATTTTCCATCTAACTGGACCTTGCCCAACATTG
CCAGTTTATGAAAGTGATCCTGTTTTTCATCGATGTATTCCAACTGGAAAAAATGCACCA
ATCAAAGAGGCTCAAGAATTATTCAATGTAGTTTCAGGTTGGGACTTTGTAGAAAAAACT
GCACACGATTTATACAAATCTTGGCATGTGATTGCTCTCGTTTGTGGTTTGAGTTTAATT
TTTTCAATCATTCTCATCGGATTACTTCACTACCTTACACAAATTATTTCTTGGCTGATT
TGCATTTTTGTTGGAGTTGCTAGCATTGCCATTACTATTTTATTATGGTACACATATTTT
GAAATTAAGAAGAAGAAAGATTCATCCGAACTATCTCAACTTGCTCAATATCTTCAAAAT
GAAACTGCTGTATATGTCTTTGCCATCATTGCTACAATCGTCATGATAATTTTGATTGTC
GTCATCTACTTCATGTCATCAAAGTTTTCAGGGTTGGCAGCATTATTTGAAGAAGCTGGC
AAATGCATTTACTCGATGCCACAAATATTTGGACCACCACTTCTTGCATTCATCGCACTC
ATGATTTTCTTTGCATTTTGGGTCACAGTTGTTGTTTGTCTTGCAACTGCAGCAATTCCT
GGATTCAAACCAATTTTAGATGTGACAAATCCTCAAGAAAATATTCCAAAAGATCCAAAG
AATGGCGCTGATTTACAAAAAACTTTCAAACTCGTTGAATATCAAGAAGTTGACTATACA
AGATACATGCTTTACATCTACCTCGTTGCACTCGTCTGGGTTTCTGAGTTTATTTTTGCT
GCTTCTCAATTATGTCTTGCCGGTGCTGTTGCATTATGGTATTTCAAAAAACCAACAGAT
TCACCAGTTTGTGATTCTATGAGCAAGCTTATTAAATATCATCTTGGATCAGTTGCAAAA
GGCTCTTTTTTGATCACTCTCTTCAAAATTCCTCGATTGATTTTGAGCTATCTTTATGCA
AAATTAAAGGCTTATTCACGAGATGGTAATAGCGTTGCAGATTGTTGTCTTAAATGTTGC
ATTTGCTGCTTCTGGTGTCTTGAAAAATTTATTCGTTATTTGAACCATAATGCTTATACT
GTCATTGCCATTGAAAGTATTAACTTTTGCCCGGCTGCCGGAGTTGCTTGGAAGGCGATT
TGGACGCATGTTGTCAGCGTTGGTACAATAAATAGTATTGGAGATTTAGTACTTTTCTTG
GGAAAACTTGCTGTTTCTGGAATTTGTGGCTTCATTGCTTTACTCTTTTTGAAAAATGAT
TCTGAAATTCAATTCTACATGGTTCCAGTATTTATCATTGCTCTATTTGCTTTCTTTGTG
GCTCATGTCATTTTGTCACTTTATGAAATTGTCGTTGATACTCTCTTCTTGTGCGTTTAT
GAAGATCGCCATATTAATGGACCAAATGGTCGTTGGAAAGAATCAAATTTGGCCAATTTG
TTGGGTGAAGAAAAAGCTGTTGCAGTTGAAGGTCAAATGCATGAAGTCGAACTGCAACCA
ATCACCAGACAACCTTTCGGCCATTACCGTGAAGCTCAACCAACTACCTTACCAGTTTAA
>g8427.t1 Gene=g8427 Length=679
MGCFESKQNRTDPVAVRGCTDVCWLVIFILFWVLLIVIAAFAFVYGNPQRIINGYDSFGN
TCGVSDNKNYADISYGKAAGIDTSDKKFVYFFNIKEIKKSLKICVKQCPSKQLNTSVQLY
DYYREKDTSYCRYDFDMNKLTRASDNDELIFHLTGPCPTLPVYESDPVFHRCIPTGKNAP
IKEAQELFNVVSGWDFVEKTAHDLYKSWHVIALVCGLSLIFSIILIGLLHYLTQIISWLI
CIFVGVASIAITILLWYTYFEIKKKKDSSELSQLAQYLQNETAVYVFAIIATIVMIILIV
VIYFMSSKFSGLAALFEEAGKCIYSMPQIFGPPLLAFIALMIFFAFWVTVVVCLATAAIP
GFKPILDVTNPQENIPKDPKNGADLQKTFKLVEYQEVDYTRYMLYIYLVALVWVSEFIFA
ASQLCLAGAVALWYFKKPTDSPVCDSMSKLIKYHLGSVAKGSFLITLFKIPRLILSYLYA
KLKAYSRDGNSVADCCLKCCICCFWCLEKFIRYLNHNAYTVIAIESINFCPAAGVAWKAI
WTHVVSVGTINSIGDLVLFLGKLAVSGICGFIALLFLKNDSEIQFYMVPVFIIALFAFFV
AHVILSLYEIVVDTLFLCVYEDRHINGPNGRWKESNLANLLGEEKAVAVEGQMHEVELQP
ITRQPFGHYREAQPTTLPV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g8427.t1 | PANTHER | PTHR12385:SF12 | SOLUTE CARRIER FAMILY 44 MEMBER 1A-RELATED | 7 | 649 | 3.6E-225 |
| 3 | g8427.t1 | PANTHER | PTHR12385 | CHOLINE TRANSPORTER-LIKE (SLC FAMILY 44) | 7 | 649 | 3.6E-225 |
| 1 | g8427.t1 | Pfam | PF04515 | Plasma-membrane choline transporter | 289 | 623 | 8.7E-88 |
| 23 | g8427.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 23 | - |
| 30 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 24 | 45 | - |
| 17 | g8427.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 46 | 207 | - |
| 25 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 208 | 229 | - |
| 22 | g8427.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 230 | 234 | - |
| 31 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 235 | 262 | - |
| 16 | g8427.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 263 | 282 | - |
| 24 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 305 | - |
| 20 | g8427.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 306 | 333 | - |
| 29 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 334 | 359 | - |
| 14 | g8427.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 360 | 403 | - |
| 32 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 404 | 435 | - |
| 19 | g8427.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 436 | 454 | - |
| 26 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 455 | 480 | - |
| 18 | g8427.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 481 | 555 | - |
| 27 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 556 | 577 | - |
| 21 | g8427.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 578 | 582 | - |
| 28 | g8427.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 583 | 605 | - |
| 15 | g8427.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 606 | 679 | - |
| 11 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 24 | 46 | - |
| 8 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 208 | 230 | - |
| 9 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 235 | 257 | - |
| 4 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 305 | - |
| 13 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 333 | 355 | - |
| 12 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 411 | 433 | - |
| 5 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 453 | 475 | - |
| 7 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 519 | 541 | - |
| 6 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 556 | 578 | - |
| 10 | g8427.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 585 | 607 | - |
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:0055085 | transmembrane transport | BP |
| GO:0022857 | transmembrane transporter activity | MF |
KEGG
Orthology
- This transcript has been annotated with K06515 (solute carrier family 44 (choline transporter-like protein), member 1)
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.
