RetrogeneDB ID: | retro_cjac_3328 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:96381710..96382749(-) | ||
| Located in intron of: | ENSCJAG00000014985 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HMMR | ||
| Ensembl ID: | ENSCJAG00000015371 | ||
| Aliases: | None | ||
| Description: | hyaluronan-mediated motility receptor (RHAMM) [Source:HGNC Symbol;Acc:5012] |
Retrocopy-Parental alignment summary:
>retro_cjac_3328
ACAGAAAAACTCTTAGAATATATCCAAGAAATTAGTTGTGCTTCAGACCAAGTGGAAAAATACAATCTAGATATTGCCCA
GTTAGAAGAAAATTTGAAGAAGAATCATGACATTTTAAGGCTTAAGCAGTATATTGAGGAAAATACTGTTATATTATCTA
AACAAGAAGAAGACCTAAATGCAAAAGGTCAGCTGCTTGAAAAAGAAAAAGAAGATCATGTCAACAGGAATAGAGAACAT
AATGAATATCTAAATGCTGAGATGCAAAACCTAAAACAGAAGTTTATTCTTGAACAACAGGAACGTGAAAAGCTTCAACA
AAAGGAATTACAAGAATTATCTTCTAGTCTTCATCAGTTGTGTTCTTTTCAAGAGGAGATGGTTAAAGAGAAGAATCTCT
TTGAGGAAGAATAAAAACAAGCACTGGATGAACTTGATAAATTACAGCAAAAGGAGGAACAATCTGAAAGGCTGGTCAAG
CAATTGGAAGAGGAAACAAAATCTAGAGCTGAAGAATTAAAACTCCTAGAAGAAAAGCTGAAAGGGAAAGAGGCTGAACT
GGAGAAAAGTAGTGCTGCTCATACCCAGGCCACTCTGCTTTTGCAGGAAAAGTTTAACAGTATAGTGCAAAGCCTTGAAG
ATGTTACTGCTCAATTTGAAAGCTATAAAGCATTAACAGCCAGTGAGATAGAAGATCTTAAGCTGCAGAACTCATCATTA
CAGGAAAAAATGGCCAAGGCTGGAAAAAATGCAGAAGATATTCAGGGTGTGGCAACCGAGAGCTCAAGTCAAGAATATGC
AAGGATGCTTCTAGATCTACAGCCCAACTCAGCACTAAAAGAAAGAGAAATTAAAGAAATCAGTTTCTTCTTTTCAAAAA
ATAACTGATTTGCAGAACCAACTCAAGCAACAAGAGGAAGATTTTAGAAAACAACTGGAAGATGAAGCAGCAAGAAAAGC
TGGAAACACAACGGCACAATTAACTGAAGAAATTAACAAGTGGCGTCTCCTTTACAAAGGACTGTATAATAAAATAAAA
ORF - retro_cjac_3328 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.32 % |
| Parental protein coverage: | 56.77 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SDQVEKYKLDIAQLEENLKEKNHEILSLKQSLEENTVILS-KQVEDLNVKCQLLEKEKEDHVNKNREHNE |
| ......Y...I..........N..I..L...L..N..IL..KQ....N....L...E............E | |
| Retrocopy | TEKLLEYIQEISCASDQVEKYNLDIAQLEENLKKNHDILRLKQYIEENTVI-LSKQEEDLNAKGQLLEKE |
| Parental | NLNAEMQNLKHKFILEQQELEKLQQK---ELQVNSLLQQEK--ELSSSLHEKLCSFQEEMVKEKNLFEEE |
| .......N..H...L...E...L.QK...E.Q....LQQ....ELSSSLH..LCSFQEEMVKEKNLFEEE | |
| Retrocopy | KEDHVNRNREHNEYLNA-EMQNLKQKFILEQQEREKLQQKELQELSSSLHQ-LCSFQEEMVKEKNLFEEE |
| Parental | LKQALDELDKLQQKEEQSEQLVKQLEEETKSRAEELKLLEEKLKGKEAELEKSSAAHTQATLLLQEKYNS |
| .KQALDELDKLQQKEEQSE.LVKQLEEETKSRAEELKLLEEKLKGKEAELEKSSAAHTQATLLLQEK.NS | |
| Retrocopy | *KQALDELDKLQQKEEQSERLVKQLEEETKSRAEELKLLEEKLKGKEAELEKSSAAHTQATLLLQEKFNS |
| Parental | TVQSLEDVTAQFESYKALTASEIEDLKLQNSSLQEKLAKAGKNADDIQGQILATESSNQEYARLLLDLQT |
| .VQSLEDVTAQFESYKALTASEIEDLKLQNSSLQEK.AKAGKNA.DIQG...ATESS.QEYAR.LLDLQ. | |
| Retrocopy | IVQSLEDVTAQFESYKALTASEIEDLKLQNSSLQEKMAKAGKNAEDIQG--VATESSSQEYARMLLDLQP |
| Parental | KSALKEREIKEITVSSFQK-ITDLQNQLQQQEEDFRKQLEDEEARKAGKENKMAQLTEEINKWRLLYEEL |
| .SALKEREIKEI....F.K.ITDLQNQL.QQEEDFRKQLEDE.ARKAG..N..AQLTEEINKWRLLY..L | |
| Retrocopy | NSALKEREIKEISF-FFSK>ITDLQNQLKQQEEDFRKQLEDEAARKAG--NTTAQLTEEINKWRLLYKGL |
| Parental | YNKVK |
| YNK.K | |
| Retrocopy | YNKIK |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .18 RPM | 8 .74 RPM |
| SRP051959_heart | 0 .28 RPM | 4 .82 RPM |
| SRP051959_kidney | 0 .35 RPM | 2 .64 RPM |
| SRP051959_liver | 0 .11 RPM | 2 .73 RPM |
| SRP051959_lung | 0 .42 RPM | 5 .60 RPM |
| SRP051959_lymph_node | 0 .32 RPM | 8 .74 RPM |
| SRP051959_skeletal_muscle | 0 .11 RPM | 4 .45 RPM |
| SRP051959_spleen | 0 .27 RPM | 8 .42 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3328 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3328 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3328 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000017192 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000015371 | 1 retrocopy |
retro_cjac_3328 ,
|
| Myotis lucifugus | ENSMLUG00000001674 | 1 retrocopy |