RetrogeneDB ID: | retro_cjac_2618 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:63573336..63573744(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ITGB3BP | ||
| Ensembl ID: | ENSCJAG00000016555 | ||
| Aliases: | None | ||
| Description: | integrin beta 3 binding protein (beta3-endonexin) [Source:HGNC Symbol;Acc:6157] |
Retrocopy-Parental alignment summary:
>retro_cjac_2618
AATCTGTTTGCTTTTCCCACAAGCTCTAAAGAACAAGAGTACCAAAATGGACTATCAAATGAAAAGAGAAAAAAATTGAA
TTACCCCAGTTTAATTGAAAGCAAAGAATCTACAACAAAAGTCAGTGATGAATTCGTGATCTTGCTGTCTAAAGTTGAGA
AATTGTCAGAAGAAATTGTGGAGATAATGCAAAATGTAAGTCATATGCAGGCTTCAGAGGGCAGGAGAGAGCCTGAAAAT
CTCACTGGAATCTCCTGTGGATCACGTTTCTTAAAAAGAGAAATGCAGAAAACCAAAGAACTAATGACAAAAGTAACTAA
AGAAAAACTGTTTGAAAAGAGTTGAGGACTTCCTCACAGAGAATCATGTCATCATGACAGCTGTGAATTCCTTAAAGTCA
TTTTAAAC
ORF - retro_cjac_2618 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.09 % |
| Parental protein coverage: | 76.84 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SLFASPTSSKEQEYGNGLSNEKRKKLNHPSLTESKESTTKDNDEFMMLLSKVEKLSEEIVEIMQNLSSIQ |
| .LFA.PTSSKEQEY.NGLSNEKRKKLN.PSL.ESKESTTK..DEF..LLSKVEKLSEEIVEIMQN.S..Q | |
| Retrocopy | NLFAFPTSSKEQEYQNGLSNEKRKKLNYPSLIESKESTTKVSDEFVILLSKVEKLSEEIVEIMQNVSHMQ |
| Parental | ALEGSRELENLIGISCGSRFLKREMKKTKELMTKVTKRKLFEKSSVLPHRESCHLDSYEFLKAILN |
| A.EG.RE.ENL.GISCGSRFLKREM.KTKELMTKVTK.KLFEKS..LPHRESCH.DS.EFLK.ILN | |
| Retrocopy | ASEGRREPENLTGISCGSRFLKREMQKTKELMTKVTKEKLFEKS*GLPHRESCHHDSCEFLKVILN |
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 .00 RPM | 2 .51 RPM |
| SRP051959_heart | 0 .00 RPM | 1 .09 RPM |
| SRP051959_kidney | 0 .00 RPM | 1 .62 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .15 RPM |
| SRP051959_lung | 0 .00 RPM | 1 .72 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .97 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .96 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .31 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2618 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2618 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2618 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000030710 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000016555 | 3 retrocopies |
retro_cjac_2618 , retro_cjac_3850, retro_cjac_3991,
|
| Mus musculus | ENSMUSG00000028549 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000009116 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000007480 | 1 retrocopy |