General information for g5678.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-binding cassette sub-family A member 3.
Parent gene
- The parent gene g5678 is located on chr_2: 11228091..11229016 (- 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 | g5678 | g5678.t4 | isoform | g5678.t4 | 11227076 | 11229016 |
| chr_2 | g5678 | g5678.t4 | exon | g5678.t4.exon1 | 11227076 | 11227492 |
| chr_2 | g5678 | g5678.t4 | cds | g5678.t4.CDS1 | 11227077 | 11227492 |
| chr_2 | g5678 | g5678.t4 | exon | g5678.t4.exon2 | 11227551 | 11227989 |
| chr_2 | g5678 | g5678.t4 | cds | g5678.t4.CDS2 | 11227551 | 11227989 |
| chr_2 | g5678 | g5678.t4 | exon | g5678.t4.exon3 | 11228091 | 11228468 |
| chr_2 | g5678 | g5678.t4 | cds | g5678.t4.CDS3 | 11228091 | 11228468 |
| chr_2 | g5678 | g5678.t4 | exon | g5678.t4.exon4 | 11228536 | 11229016 |
| chr_2 | g5678 | g5678.t4 | cds | g5678.t4.CDS4 | 11228536 | 11228823 |
| chr_2 | g5678 | g5678.t4 | TSS | g5678.t4 | 11229039 | 11229039 |
| chr_2 | g5678 | g5678.t4 | TTS | g5678.t4 | NA | NA |
Sequences
>g5678.t4 Gene=g5678 Length=1715
ATGTGGTCGCATAAATTTAAGCTTCTACTATGGAAGAACTGGATTTTAGTAAAAAGACAT
CCGATTGCTGGTATTTTATAGTTTGAAATTACAATAATAAAGAATAAAAATTTTAAAAAT
TATTTTTTCAACAGGATTGTTTGAGATAGTTTTTCCAGTTTTAATTGTTCTAATTTTCAC
ATATTCTCGTGGGATGGTTGGGAGCTCAAAAATACCAGAAGTTCACTATGAATCATTCGA
TACATTTCCAACACAATGCAGTTTTGGATATTCATTTAAAGAAGATTATATTGAAAAAAT
TGGATATGCACCGGAAACTGAATTTTTTACGAATATTATAACAAATGCAATTCAAAATAA
GGAGTCTAAATCAAAATTAAAAATTTTTCCTTTTAAAAATGAAGACGAACTTAATATATG
GATACGAAATGAGTCTGCTACGTCACCAGTTGCTGCAGTTTTCTTCGAAGAAATTGATGC
AATAACGAAAAATAACAATGAGATTTCACCGAAACATTTGAAGTATGTTATTCATATGCC
TCAAGATTCAACAACAGACTCGTGGTTTACGGATCAAATTTATTACTCAAGTCCATCCAA
AAGATCTCGCTTATCAGAGCATTCTAGTGGCGTACCCAACACACCACCTTATTATGGTTC
ATGCTTTCTTGATATACAAAATCATATTGACAGAGCATTTATAAAGTATTTAAATTCATC
GGCAACTTTTCCAAAACTCAAAATGAATGCTTTTCCTTATCCAGAAATTATTGAAGATAT
TTTCATGCAATTTGCAACTCAAGCATTTCCAGTACTTTTTGTACTATGCATGATGTTGTC
AATTAAAAACATTATTAAGAATATAGCAATAGAGCGAGAAACATTGTTAAAAGAATCTAT
GAAAATGATGGGTTTGAGCTCGATGATGCACTGGATTTCATGGTTAACAAAATGCTTTAT
AATGTTAATAATACCCTTTACTTTCAACTGTATACTGATGACAACCACACTTGCAAGCGA
ATTACCATTATTTGTAAACAGTAATCCTATTTTAATATGGATATTTCTAGTGATATACAT
CTTTTCGGTTGTAACGTTATGTTTCTTAATTGCTGTTTGTTTTGAGAAATCAACGAATGC
AGCAAACGTTGGGACATTAATTTTTTTCATTGCTATTGTTCCTCACATTTATTTTGCGGA
AAAGTTTCATGCTTTTCCATATATTCTAAAAGCTGTTTATAGCATGATACCTAATTCGAA
TATGGGTTTAGCTGTTTCTATTTTGGCAAATTCTGAAGCTACTGAAACAGGAATTGGAAT
AACCACTTTATTCAAGAGAAGTGTCGATTTGAAATTTTCATTTGGAGAAATTTTAATTTT
CATGATTCTCGGAAGTATTATTCAAATGTTTCTAGCAACATACATTGAACGAGTTTTCCC
AGGTGAATTTGGAATTTCGGATCCTTTTTATTATCCTGTTATGCCATTCATTAAATTTAT
TAAGCGACAAATGGGATATGATTCATTATCGAATGAATCTGTTCTTCAAGATAGACGAAT
CTCAAATCAAGACTATGAAGAAGAACCTGAAAATTTACGAGCTGGTGTTAGAATTGTCAA
TTTAAGTAAAAAATTCGGTGATAAATTTGTTGTTGATAAACTTTGTCTAAATATGTTTGA
AGATCAAATAACAGTATTATTAGGACATAATGGAG
>g5678.t4 Gene=g5678 Length=507
MVGSSKIPEVHYESFDTFPTQCSFGYSFKEDYIEKIGYAPETEFFTNIITNAIQNKESKS
KLKIFPFKNEDELNIWIRNESATSPVAAVFFEEIDAITKNNNEISPKHLKYVIHMPQDST
TDSWFTDQIYYSSPSKRSRLSEHSSGVPNTPPYYGSCFLDIQNHIDRAFIKYLNSSATFP
KLKMNAFPYPEIIEDIFMQFATQAFPVLFVLCMMLSIKNIIKNIAIERETLLKESMKMMG
LSSMMHWISWLTKCFIMLIIPFTFNCILMTTTLASELPLFVNSNPILIWIFLVIYIFSVV
TLCFLIAVCFEKSTNAANVGTLIFFIAIVPHIYFAEKFHAFPYILKAVYSMIPNSNMGLA
VSILANSEATETGIGITTLFKRSVDLKFSFGEILIFMILGSIIQMFLATYIERVFPGEFG
ISDPFYYPVMPFIKFIKRQMGYDSLSNESVLQDRRISNQDYEEEPENLRAGVRIVNLSKK
FGDKFVVDKLCLNMFEDQITVLLGHNG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5678.t4 | PANTHER | PTHR19229:SF36 | ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 3B | 88 | 507 | 1.7E-62 |
| 3 | g5678.t4 | PANTHER | PTHR19229 | ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA | 88 | 507 | 1.7E-62 |
| 1 | g5678.t4 | Pfam | PF12698 | ABC-2 family transporter protein | 64 | 408 | 1.4E-14 |
| 12 | g5678.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 203 | - |
| 17 | g5678.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 226 | - |
| 11 | g5678.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 227 | 246 | - |
| 15 | g5678.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 247 | 274 | - |
| 14 | g5678.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 275 | 285 | - |
| 19 | g5678.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 286 | 310 | - |
| 9 | g5678.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 311 | 316 | - |
| 16 | g5678.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 317 | 335 | - |
| 13 | g5678.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 336 | 392 | - |
| 18 | g5678.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 393 | 411 | - |
| 10 | g5678.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 412 | 507 | - |
| 7 | g5678.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 226 | - |
| 5 | g5678.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 247 | 271 | - |
| 6 | g5678.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 286 | 308 | - |
| 8 | g5678.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 315 | 334 | - |
| 4 | g5678.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 388 | 410 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5678/g5678.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5678.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0055085 | transmembrane transport | BP |
| GO:0042626 | ATPase-coupled transmembrane transporter activity | MF |
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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