General information for g9816.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CTL-like protein 2.
Parent gene
- The parent gene g9816 is located on chr_1: 5375736..5377414 (- 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 | g9816 | g9816.t1 | TTS | g9816.t1 | 5375375 | 5375375 |
| chr_1 | g9816 | g9816.t1 | isoform | g9816.t1 | 5375736 | 5377414 |
| chr_1 | g9816 | g9816.t1 | exon | g9816.t1.exon1 | 5375736 | 5375827 |
| chr_1 | g9816 | g9816.t1 | cds | g9816.t1.CDS1 | 5375736 | 5375827 |
| chr_1 | g9816 | g9816.t1 | exon | g9816.t1.exon2 | 5375889 | 5376868 |
| chr_1 | g9816 | g9816.t1 | cds | g9816.t1.CDS2 | 5375889 | 5376868 |
| chr_1 | g9816 | g9816.t1 | exon | g9816.t1.exon3 | 5376923 | 5377151 |
| chr_1 | g9816 | g9816.t1 | cds | g9816.t1.CDS3 | 5376923 | 5377151 |
| chr_1 | g9816 | g9816.t1 | exon | g9816.t1.exon4 | 5377411 | 5377414 |
| chr_1 | g9816 | g9816.t1 | cds | g9816.t1.CDS4 | 5377411 | 5377414 |
| chr_1 | g9816 | g9816.t1 | TSS | g9816.t1 | NA | NA |
Sequences
>g9816.t1 Gene=g9816 Length=1305
ATGCGAGTTGTTCAGAGTTACCGTCAATATGATTTCTTTTCAAAAAATCCCGAAGATCGT
ATCAATTTGCAACCGAATTTAAAATCGTTCATAAATTCATATCTTGCAAAATCTGACACA
TGGCTTTACATTCTCATCGCTTTATCAATCATACTTGTTGTGATTTTGCTATTGATTATT
GTGTTCCGCAAGAGAATTGTTATTGCAATTGCTCTTATTAAAGAAGGAAGCAAAGCTGTG
TCATCGAATTTATCAACAGTTTTCTTTCCTATTGTACCATGGCTATTGCAAATATCTGTA
ATTGTTCTCTCAATTTTGATGTTCCTTTATTTATCATCAATTGGAGAACCATCATATAAA
ATAGTTGGTATGAATAAGACAAGTTGTGTCTGCACTGGAGAGTATTCAACAATCAAAAAT
GGCGACTCATGCAATCAAACTAAATTTTTGAACTATTGTTCAAATTTAGGACCTGAATGT
TCAACTGTATCATGTCATTATATCGGATTGAATGCACCACAAATTGCTCAATATTTCAAA
TACATTACTATCGTTGGTTTCTTTTGGCTTTTGTTTTTCATATCAGGCTTCTCAGAGATG
GTTTTAGCTGGAACATTTTCTGAATGGTATTGGACAATAAACAAAGCTGATGTACCATTT
TTCACATTAAGTGCAAGTATTTATCGAACAATTCGTTTTCATCTCGGAACAATTGCCTTT
GGATCGTTGATCCTAACAATTTGTCGCATCATTCGTTTGATTATTGAGTATATCGATCAA
AAACTTAAGAAATACAACAATGAACTGACACGTGCGATTTTGTGTTGCTGCCGATGCTTT
TTCTGGTGTCTTGAAAACTTTCTCAAATTTCTTAATCGCAATGCTTACATTATGTGTGCA
ATTCATGGCAAGAACTTTTGCTCAAGTGCAAGAGATGCTTTCAATTTGCTGATGCGAAAT
GTACTTAGAGTTATTGCTCTTGATAAGACAACCGATTTTCTATTTTTCTTGTCAAAATTG
CTGATTTCACTTGGAATGGCTGCCTGTACTTTCACCTATCTTACAAGTGAACTTTTCAAT
AACCATTTCCCTGATATTCTACTTCATTATCCAATTGTTCAAGTTGGATTTATTTTTGTT
GGATCTTACATCATTGCTTCTGTATTCTTCAGTGTTTATTCAATGGCTGTCGATACACTC
TTCTTATGCTTCCTTGAAGATTGTGAACGTAATGATGGAAGTCAAGATCGTCCATATTTC
ATGAGTAAACAGTTGATGAAAATTCTCAACAAAACAAACAAGTAA
>g9816.t1 Gene=g9816 Length=434
MRVVQSYRQYDFFSKNPEDRINLQPNLKSFINSYLAKSDTWLYILIALSIILVVILLLII
VFRKRIVIAIALIKEGSKAVSSNLSTVFFPIVPWLLQISVIVLSILMFLYLSSIGEPSYK
IVGMNKTSCVCTGEYSTIKNGDSCNQTKFLNYCSNLGPECSTVSCHYIGLNAPQIAQYFK
YITIVGFFWLLFFISGFSEMVLAGTFSEWYWTINKADVPFFTLSASIYRTIRFHLGTIAF
GSLILTICRIIRLIIEYIDQKLKKYNNELTRAILCCCRCFFWCLENFLKFLNRNAYIMCA
IHGKNFCSSARDAFNLLMRNVLRVIALDKTTDFLFFLSKLLISLGMAACTFTYLTSELFN
NHFPDILLHYPIVQVGFIFVGSYIIASVFFSVYSMAVDTLFLCFLEDCERNDGSQDRPYF
MSKQLMKILNKTNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g9816.t1 | PANTHER | PTHR12385 | CHOLINE TRANSPORTER-LIKE (SLC FAMILY 44) | 6 | 434 | 1.4E-157 |
| 3 | g9816.t1 | PANTHER | PTHR12385:SF90 | CTL-LIKE PROTEIN 2 | 6 | 434 | 1.4E-157 |
| 1 | g9816.t1 | Pfam | PF04515 | Plasma-membrane choline transporter | 46 | 409 | 1.6E-103 |
| 11 | g9816.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 40 | - |
| 17 | g9816.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 41 | 62 | - |
| 15 | g9816.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 63 | 90 | - |
| 20 | g9816.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 91 | 111 | - |
| 13 | g9816.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 112 | 186 | - |
| 19 | g9816.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 211 | - |
| 16 | g9816.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 212 | 230 | - |
| 21 | g9816.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 255 | - |
| 10 | g9816.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 256 | 332 | - |
| 18 | g9816.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 333 | 354 | - |
| 14 | g9816.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 355 | 365 | - |
| 22 | g9816.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 366 | 392 | - |
| 12 | g9816.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 393 | 434 | - |
| 6 | g9816.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 40 | 62 | - |
| 5 | g9816.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 92 | 114 | - |
| 4 | g9816.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 181 | 203 | - |
| 8 | g9816.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 233 | 255 | - |
| 9 | g9816.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 333 | 355 | - |
| 7 | g9816.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 370 | 392 | - |
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 K15377 (solute carrier family 44 (choline transporter-like protein), member 2/4/5)
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.
