General information for g16261.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cubilin-like protein.
Parent gene
- The parent gene g16261 is located on chr_4: 8897313..8907303 (- 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_4 | g16261 | g16261.t1 | isoform | g16261.t1 | 8897313 | 8907303 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon1 | 8897313 | 8897666 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS1 | 8897313 | 8897666 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon2 | 8902734 | 8902939 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS2 | 8902734 | 8902939 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon3 | 8903572 | 8903630 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS3 | 8903572 | 8903630 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon4 | 8903848 | 8904397 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS4 | 8903848 | 8904397 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon5 | 8904453 | 8904481 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS5 | 8904453 | 8904481 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon6 | 8904616 | 8904741 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS6 | 8904616 | 8904741 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon7 | 8904942 | 8905211 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS7 | 8904942 | 8905211 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon8 | 8905298 | 8905552 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS8 | 8905298 | 8905552 |
| chr_4 | g16261 | g16261.t1 | exon | g16261.t1.exon9 | 8907284 | 8907303 |
| chr_4 | g16261 | g16261.t1 | cds | g16261.t1.CDS9 | 8907284 | 8907303 |
| chr_4 | g16261 | g16261.t1 | TSS | g16261.t1 | NA | NA |
| chr_4 | g16261 | g16261.t1 | TTS | g16261.t1 | NA | NA |
Sequences
>g16261.t1 Gene=g16261 Length=1869
ATGAAAAATTTTAAAAAAAAAATTAATCGAAGAATTAACAATCTTGAGCAAAGGTTGGCA
AATTTAACAGAAAGATTGACAAAAGATCATTGTAAAAGTTATCCATGTCAAAATGGTGGA
ACTTGTTTTAATTTATACGACACTCGATGTGAATGTAGAGAAAATTATGAAGGACCACAA
TGTACTCTTGATGTTAATGAATGTGCAAGATATGCTGGAACTGATTTAGGTTGTCAAAAT
GGAGCTACTTGTATAAATACTGTTGGATCTTATGAATGCATTTGCCCAGAACACTGGACT
GGCATTCATTGCAACCGTAGAAAAGTTGATTGTCTTTCAGTACCACAATCTGAAATTTGT
GGTCAAGGAATTTGTGTCCATGACAATAATAAAGATGGATATTCTTGTATTTGTAATCAA
GGATGGAAGAAAGACAACAACAGTCGAGCTTGTACGCAAGATGTTGATGAATGTCAAGAA
ATGAGACCTCATTGTTCTGTTGATCCTCCTGTGCTTTGTGTTAATACACCTGGGTCTTTT
GTTTTTCCTTGTCCTGCTGGTTATCGTGGAAATGGTTACTTCTGTAGAGACATTGATGAA
TGTGAAGTCAATAACGGAGGTTGTAGTATATCACCGAAAGTTGAATGTTTAAATACTTAT
GGATCTTTCCGTTGTGGTCAATGTCCTCTTGGTTATGAAGACAGCAGTATTTGTAACTCT
AATGCAATTTGTGTTCAATATCCAAATTCACCACCATCGTGCACATGCAAATTTGGTTTC
ACTGGCAACGGATTTGGTGATAATGGCTGCGTTCCTATGGCACCTGATCCATGCGTGGCA
CTTTTTTGTCGTAATGGAGGAACTTGCATTCGAAATGGAACTCATCCTTATTGCAGTTGT
CCACCAGGCACAAGTCCACCATTATGTGATAGAACTAGAAATGGTTGTGATCCAAATCCT
TGTCGCAATGGAGGAAATTGCACAACTATGAGATTTGGTTTTGGTTTTCGATGCACATGC
CCTCGTGGATTTATTGGTGTTCGATGTGAAAATCAACAGTCAACATGTGGAGGCGTAATA
AGTACTGAAAATGGAACTCTGCGATATCCAACTGATCCAACAGCGACAACTTATCAACAT
AATTCGAGATGTGCATGGCTTATTAGAACAAACATTACAAAAGTATTAAATATCACTTTC
ACATCATTTATATTGAATTCAGTAATGAATGTCGATATGATTGGCTTCAAATCAGACAAT
AGCACAGCTCATGATGGATTCGAATTGAAATGGGAATCAATTGATCCGGTTATTGAAGGA
ATTCCAGGATGTGGTGGAATATATACGGCAGCTAAAGGTGACATTTCTTCACCAATGGAT
ATTAATGATGGAACTTATAAACATAACTTATTATGTGATTATGTCATAAGAATGCAACTG
ACACAAGAATTAGAATTGAATTTAAGAAATTTGGACTTGAAAGAAAGTTCAACTTGTAAA
TTTGATGCAGTTGAGAAAATTCATCCTTGTTTGCTTCATTTTTTCGATGGTACAAATGAT
TTCTTGATTTTGGAAAATCTAAATGATTGTGGATATTTTTCATCTCCACGTCAAAAAACC
AATGGCCTGAATTTAAGCCGGTTTATAATGCAAACTCTTGGCCGATTCCATGGAATGTCA
TTCATAATTCGAGATCAAGATCCAGAATTATTTAAAGAACTTTCAACAGTCCTGAAGAAA
CTTATCATTCAAATCGCTTTAAAACTTGGCATTGAAATTTCATTGATATTCAAACTGATA
TTGCACTTTGATGCACTTTCGAAATATTATGGTGGAACTAAATTGAAGCAAGAGGAAAGA
AATTTTTAA
>g16261.t1 Gene=g16261 Length=622
MKNFKKKINRRINNLEQRLANLTERLTKDHCKSYPCQNGGTCFNLYDTRCECRENYEGPQ
CTLDVNECARYAGTDLGCQNGATCINTVGSYECICPEHWTGIHCNRRKVDCLSVPQSEIC
GQGICVHDNNKDGYSCICNQGWKKDNNSRACTQDVDECQEMRPHCSVDPPVLCVNTPGSF
VFPCPAGYRGNGYFCRDIDECEVNNGGCSISPKVECLNTYGSFRCGQCPLGYEDSSICNS
NAICVQYPNSPPSCTCKFGFTGNGFGDNGCVPMAPDPCVALFCRNGGTCIRNGTHPYCSC
PPGTSPPLCDRTRNGCDPNPCRNGGNCTTMRFGFGFRCTCPRGFIGVRCENQQSTCGGVI
STENGTLRYPTDPTATTYQHNSRCAWLIRTNITKVLNITFTSFILNSVMNVDMIGFKSDN
STAHDGFELKWESIDPVIEGIPGCGGIYTAAKGDISSPMDINDGTYKHNLLCDYVIRMQL
TQELELNLRNLDLKESSTCKFDAVEKIHPCLLHFFDGTNDFLILENLNDCGYFSSPRQKT
NGLNLSRFIMQTLGRFHGMSFIIRDQDPELFKELSTVLKKLIIQIALKLGIEISLIFKLI
LHFDALSKYYGGTKLKQEERNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 30 | g16261.t1 | CDD | cd00054 | EGF_CA | 29 | 62 | 7.12123E-4 |
| 32 | g16261.t1 | CDD | cd00054 | EGF_CA | 64 | 104 | 8.551E-9 |
| 31 | g16261.t1 | CDD | cd00054 | EGF_CA | 317 | 350 | 7.7052E-4 |
| 26 | g16261.t1 | Coils | Coil | Coil | 5 | 32 | - |
| 18 | g16261.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 3 | 65 | 5.7E-9 |
| 23 | g16261.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 66 | 107 | 2.2E-12 |
| 22 | g16261.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 109 | 191 | 1.3E-10 |
| 19 | g16261.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 194 | 239 | 3.9E-9 |
| 21 | g16261.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 263 | 314 | 2.7E-5 |
| 20 | g16261.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 315 | 352 | 8.2E-10 |
| 24 | g16261.t1 | Gene3D | G3DSA:2.60.120.290 | - | 353 | 434 | 3.9E-7 |
| 25 | g16261.t1 | Gene3D | G3DSA:2.60.120.290 | - | 444 | 551 | 4.2E-8 |
| 9 | g16261.t1 | PANTHER | PTHR45645:SF31 | CUBILIN (INTRINSIC FACTOR-COBALAMIN RECEPTOR) | 8 | 251 | 1.6E-64 |
| 11 | g16261.t1 | PANTHER | PTHR45645 | DORSAL-VENTRAL PATTERNING PROTEIN TOLLOID-RELATED-RELATED | 8 | 251 | 1.6E-64 |
| 8 | g16261.t1 | PANTHER | PTHR45645:SF31 | CUBILIN (INTRINSIC FACTOR-COBALAMIN RECEPTOR) | 414 | 506 | 1.6E-64 |
| 10 | g16261.t1 | PANTHER | PTHR45645 | DORSAL-VENTRAL PATTERNING PROTEIN TOLLOID-RELATED-RELATED | 414 | 506 | 1.6E-64 |
| 2 | g16261.t1 | Pfam | PF00008 | EGF-like domain | 31 | 59 | 6.6E-5 |
| 1 | g16261.t1 | Pfam | PF00008 | EGF-like domain | 76 | 103 | 2.8E-8 |
| 6 | g16261.t1 | Pfam | PF07645 | Calcium-binding EGF domain | 154 | 189 | 2.1E-6 |
| 5 | g16261.t1 | Pfam | PF07645 | Calcium-binding EGF domain | 197 | 233 | 8.0E-6 |
| 3 | g16261.t1 | Pfam | PF12661 | Human growth factor-like EGF | 283 | 303 | 0.027 |
| 7 | g16261.t1 | Pfam | PF00431 | CUB domain | 444 | 505 | 2.4E-6 |
| 4 | g16261.t1 | Pfam | PF02958 | Ecdysteroid kinase | 505 | 580 | 2.6E-9 |
| 27 | g16261.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 580 | - |
| 29 | g16261.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 581 | 601 | - |
| 28 | g16261.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 602 | 622 | - |
| 49 | g16261.t1 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 50 | 61 | - |
| 53 | g16261.t1 | ProSitePatterns | PS01187 | Calcium-binding EGF-like domain signature. | 64 | 93 | - |
| 54 | g16261.t1 | ProSitePatterns | PS00010 | Aspartic acid and asparagine hydroxylation site. | 84 | 95 | - |
| 51 | g16261.t1 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 93 | 104 | - |
| 52 | g16261.t1 | ProSitePatterns | PS01187 | Calcium-binding EGF-like domain signature. | 197 | 225 | - |
| 48 | g16261.t1 | ProSitePatterns | PS01186 | EGF-like domain signature 2. | 338 | 349 | - |
| 50 | g16261.t1 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 338 | 349 | - |
| 60 | g16261.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 27 | 62 | 17.655 |
| 59 | g16261.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 64 | 105 | 18.896 |
| 58 | g16261.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 230 | 266 | 7.616 |
| 57 | g16261.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 274 | 310 | 15.406 |
| 56 | g16261.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 312 | 350 | 19.807 |
| 55 | g16261.t1 | ProSiteProfiles | PS01180 | CUB domain profile. | 444 | 505 | 9.521 |
| 39 | g16261.t1 | SMART | SM00179 | egfca_6 | 27 | 62 | 0.066 |
| 41 | g16261.t1 | SMART | SM00181 | egf_5 | 30 | 62 | 0.0065 |
| 37 | g16261.t1 | SMART | SM00179 | egfca_6 | 64 | 105 | 5.6E-11 |
| 44 | g16261.t1 | SMART | SM00181 | egf_5 | 67 | 105 | 2.2E-6 |
| 35 | g16261.t1 | SMART | SM00179 | egfca_6 | 108 | 152 | 0.14 |
| 47 | g16261.t1 | SMART | SM00181 | egf_5 | 110 | 152 | 0.017 |
| 34 | g16261.t1 | SMART | SM00179 | egfca_6 | 154 | 196 | 0.0094 |
| 46 | g16261.t1 | SMART | SM00181 | egf_5 | 157 | 196 | 120.0 |
| 36 | g16261.t1 | SMART | SM00179 | egfca_6 | 197 | 239 | 4.4E-4 |
| 43 | g16261.t1 | SMART | SM00181 | egf_5 | 200 | 239 | 24.0 |
| 42 | g16261.t1 | SMART | SM00181 | egf_5 | 240 | 271 | 190.0 |
| 38 | g16261.t1 | SMART | SM00179 | egfca_6 | 276 | 310 | 0.65 |
| 45 | g16261.t1 | SMART | SM00181 | egf_5 | 277 | 310 | 0.016 |
| 33 | g16261.t1 | SMART | SM00179 | egfca_6 | 312 | 350 | 0.73 |
| 40 | g16261.t1 | SMART | SM00181 | egf_5 | 315 | 350 | 1.3E-5 |
| 16 | g16261.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 29 | 69 | 3.57E-8 |
| 12 | g16261.t1 | SUPERFAMILY | SSF57184 | Growth factor receptor domain | 77 | 201 | 1.22E-10 |
| 13 | g16261.t1 | SUPERFAMILY | SSF57184 | Growth factor receptor domain | 155 | 303 | 9.73E-5 |
| 17 | g16261.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 314 | 352 | 4.46E-8 |
| 14 | g16261.t1 | SUPERFAMILY | SSF49854 | Spermadhesin, CUB domain | 353 | 434 | 1.83E-11 |
| 15 | g16261.t1 | SUPERFAMILY | SSF49854 | Spermadhesin, CUB domain | 443 | 505 | 3.93E-8 |
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:0005509 | calcium ion binding | MF |
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