General information for g16489.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Chondroadherin.
Parent gene
- The parent gene g16489 is located on chr_4: 9679210..9681211 (- 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 | g16489 | g16489.t1 | TTS | g16489.t1 | 9679119 | 9679119 |
| chr_4 | g16489 | g16489.t1 | isoform | g16489.t1 | 9679210 | 9681211 |
| chr_4 | g16489 | g16489.t1 | exon | g16489.t1.exon1 | 9679210 | 9679252 |
| chr_4 | g16489 | g16489.t1 | cds | g16489.t1.CDS1 | 9679210 | 9679252 |
| chr_4 | g16489 | g16489.t1 | exon | g16489.t1.exon2 | 9679314 | 9679677 |
| chr_4 | g16489 | g16489.t1 | cds | g16489.t1.CDS2 | 9679314 | 9679677 |
| chr_4 | g16489 | g16489.t1 | exon | g16489.t1.exon3 | 9679748 | 9680689 |
| chr_4 | g16489 | g16489.t1 | cds | g16489.t1.CDS3 | 9679748 | 9680689 |
| chr_4 | g16489 | g16489.t1 | exon | g16489.t1.exon4 | 9680821 | 9681211 |
| chr_4 | g16489 | g16489.t1 | cds | g16489.t1.CDS4 | 9680821 | 9681211 |
| chr_4 | g16489 | g16489.t1 | TSS | g16489.t1 | 9681233 | 9681233 |
Sequences
>g16489.t1 Gene=g16489 Length=1740
ATGAAACTTTTAATTTTTTGTTTTTCAATAATTTTTTTAACAAAAAATTCTTCGTCACAA
TTTGCAACATGTTTCTTTGGTAGTCGATCGATTGGTGGAATTTCAGTTTACTCTTGTGGT
TTTTCTATTGAAGGACATAGCAATGATGAAATTATAGAACTTGCTGGAAATCACACAACT
GGAATGAACGATGAAAATGTTCTTGGTGTCATAAATATTCAAGGATCAACAAACTTCATG
CCAAAAATTATTTGTACACGATTTCCAAATGTACAAAGAGTTCAATTTCATAGTTATGGG
TTATTAGAATTGAATGATGAAAGTTTGCAAGAGTGTCGGCAAGTGGTTTGGTTGGCAATC
AGATCTAATCCTATGATAGCAATTAGTGAAGGTACCTTTGCTAATTTAAATAATCTTATT
CATCTTGATCTTGGAACCAACACTTTAACATCACTCCCAGAAACGATTTTGTCACCTTTA
GTCAACCTACAAATTTTTGACATCAGAAACAATCATTTTAGTCAATTACCTGATAAAATT
TTCAATAATCTTCAAAATTTACGAACGCTTTTAATGCAAAATACAAGCACAACTTTTATA
AATCCTCTTTGGTTTGAAAATACTCCAAATATTGTTATGTTTCACATTTACAATAATCAA
ATTAGAGAAATTAATTCAGAAATTTTTTCCAAATTGCCATCACTTGAAAATTTGAGTCTT
AATACAAACAGAATTCAAAGAATTGGCTTTGGAACTTTTTCAAATTCTAGAAATATAACA
ATATTAAATATTGGTTCAAATAACATCACAGAAATTATCGAAGGCGATTTTGTTGGAATG
GAAAATTTACGAACTTTACAACTTTTTGATAATCCAATTGAAAGAGTTGGAAATAGAAGT
TTCTTTGGTTTAAGAAATTTAAGATTTTTAAGACTTGAAAATTGTCGAATTAGAAATCTT
GAAATAAATGCATTTGAAGGCCTTGAAGATTTGTCTGAAATCAGTTTAAGTTCAAATTTA
CTTGACGATTTACAACTTGGAATTTTTGCACCGCTTAAAAGTTTGACTTTTTTGGGTTAT
TCAAATAATCGATTTAGATTTTTACGTAGAAATATTTTTGGTGACAATTTGGCATCTTTG
ATAAATTTGGATTTAAATGAAAATCGTGTGAATGCAATTGAAAGAAGTGTCATTGAAGAA
GCTGTCAATTTGAATGTTTTACATTTTGGAAATAATGTTTGTGAAAGTGGAACTTTGAGT
AATTTTGTAACAAACAGAGTTCAACATATGGCAAGACTTGAAAGATGTTTTAGAAATTTT
GATTTTCTTGTTGACACAATCACAGAAAATTCTCCAAATTACAATTTTCATTCAACTAGT
GGTTCAGGTTTTATGGTACACGTTTATGCTGACTCAACAATTAACATTGCTTTGACACCA
TTTAATTTTCCATGGACACCAATGATTGAAATTATTATTGGAGCAGCAAACAACACAAGG
TCAATTGTTAGAAGAAATTCAGAAAATGAAGTTGTTGTGATGCCAACATTAAATGTTCTT
GAAATTAATCAATGGAATGATTTTCAAATTACTTGGGCTAATCATGTTATACTTGTGTCA
AAAGAAAACCAAATGCCATTTTTAGCATTTTCAATGCAAGATATTTTTAATGTCAATTTT
TATGGTGTTAGAACAATAGAGAGCAGAGCTATTTGGACAATTGTACCTGTTGGATTCTAA
>g16489.t1 Gene=g16489 Length=579
MKLLIFCFSIIFLTKNSSSQFATCFFGSRSIGGISVYSCGFSIEGHSNDEIIELAGNHTT
GMNDENVLGVINIQGSTNFMPKIICTRFPNVQRVQFHSYGLLELNDESLQECRQVVWLAI
RSNPMIAISEGTFANLNNLIHLDLGTNTLTSLPETILSPLVNLQIFDIRNNHFSQLPDKI
FNNLQNLRTLLMQNTSTTFINPLWFENTPNIVMFHIYNNQIREINSEIFSKLPSLENLSL
NTNRIQRIGFGTFSNSRNITILNIGSNNITEIIEGDFVGMENLRTLQLFDNPIERVGNRS
FFGLRNLRFLRLENCRIRNLEINAFEGLEDLSEISLSSNLLDDLQLGIFAPLKSLTFLGY
SNNRFRFLRRNIFGDNLASLINLDLNENRVNAIERSVIEEAVNLNVLHFGNNVCESGTLS
NFVTNRVQHMARLERCFRNFDFLVDTITENSPNYNFHSTSGSGFMVHVYADSTINIALTP
FNFPWTPMIEIIIGAANNTRSIVRRNSENEVVVMPTLNVLEINQWNDFQITWANHVILVS
KENQMPFLAFSMQDIFNVNFYGVRTIESRAIWTIVPVGF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g16489.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 70 | 293 | 2.3E-43 |
| 17 | g16489.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 294 | 552 | 4.0E-20 |
| 6 | g16489.t1 | PANTHER | PTHR46473:SF8 | ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY | 89 | 238 | 1.9E-66 |
| 10 | g16489.t1 | PANTHER | PTHR46473 | GH08155P | 89 | 238 | 1.9E-66 |
| 7 | g16489.t1 | PANTHER | PTHR46473:SF8 | ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY | 142 | 287 | 1.9E-66 |
| 11 | g16489.t1 | PANTHER | PTHR46473 | GH08155P | 142 | 287 | 1.9E-66 |
| 8 | g16489.t1 | PANTHER | PTHR46473:SF8 | ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY | 234 | 312 | 1.9E-66 |
| 12 | g16489.t1 | PANTHER | PTHR46473 | GH08155P | 234 | 312 | 1.9E-66 |
| 5 | g16489.t1 | PANTHER | PTHR46473:SF8 | ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY | 258 | 426 | 1.9E-66 |
| 9 | g16489.t1 | PANTHER | PTHR46473 | GH08155P | 258 | 426 | 1.9E-66 |
| 3 | g16489.t1 | Pfam | PF13855 | Leucine rich repeat | 114 | 173 | 7.8E-10 |
| 2 | g16489.t1 | Pfam | PF13855 | Leucine rich repeat | 233 | 293 | 1.0E-13 |
| 1 | g16489.t1 | Pfam | PF13855 | Leucine rich repeat | 305 | 365 | 8.3E-9 |
| 4 | g16489.t1 | Pfam | PF12248 | Farnesoic acid 0-methyl transferase | 476 | 568 | 1.8E-16 |
| 19 | g16489.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 20 | g16489.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 21 | g16489.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 22 | g16489.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 18 | g16489.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 579 | - |
| 26 | g16489.t1 | SMART | SM00369 | LRR_typ_2 | 136 | 159 | 0.51 |
| 24 | g16489.t1 | SMART | SM00369 | LRR_typ_2 | 160 | 183 | 0.018 |
| 29 | g16489.t1 | SMART | SM00369 | LRR_typ_2 | 232 | 255 | 0.17 |
| 27 | g16489.t1 | SMART | SM00369 | LRR_typ_2 | 280 | 303 | 14.0 |
| 31 | g16489.t1 | SMART | SM00369 | LRR_typ_2 | 304 | 327 | 0.13 |
| 28 | g16489.t1 | SMART | SM00369 | LRR_typ_2 | 328 | 351 | 9.3 |
| 30 | g16489.t1 | SMART | SM00369 | LRR_typ_2 | 352 | 375 | 11.0 |
| 25 | g16489.t1 | SMART | SM00369 | LRR_typ_2 | 377 | 400 | 43.0 |
| 13 | g16489.t1 | SUPERFAMILY | SSF52058 | L domain-like | 85 | 416 | 2.55E-51 |
| 15 | g16489.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 23 | g16489.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 14 | g16489.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 21 | - |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K06248 (chondroadherin)
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