RetrogeneDB ID: | retro_cjac_3949 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286374.1:7177..7583(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FHAD1 | ||
| Ensembl ID: | ENSCJAG00000008888 | ||
| Aliases: | None | ||
| Description: | forkhead-associated (FHA) phosphopeptide binding domain 1 [Source:HGNC Symbol;Acc:29408] |
Retrocopy-Parental alignment summary:
>retro_cjac_3949
TATGATGCCGGGCGGGATGGCTTCATCGACCTGATGGAGCTAAAGCTCATGATGGAGAAACTTGGGGCCCCCCCAGACCC
ACCTGGGCCTAAAAAGCATGATCAAGGAGGTGGATGAGGACTTTGACAGCAAGCTGAGCTTCCAGGAGTTCCTCCTGATC
TTCTGAAAGGCGGCAGCCAGGGAGCTTGAGGAGGACAGTGCGCTGTGCGTGCTGGCCCACCTCTCCGAGATCAACATCCC
CAGTGAGGGCATCGAGGGGGCCAAGACCTTCTTTGAGGCCAAGGTCCAGGCCATCAACGTGTCCAGCCGCTTTAAGGAGG
AGATCAAGTCGGAGCAGGAGGAAAGGAAGCATGCGGAGATGAAGCAGCGGAAAGCGGCCTTCAAGGAGCTGCAGTCCACC
TTTAAG
ORF - retro_cjac_3949 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.51 % |
| Parental protein coverage: | 91.95 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | YDAGRDGFIDLMELKLMMEKLGAP-QTHLGLKNMIKEVDEDFDSKLSFREFLLIFRKAAAGELQEDSGLC |
| YDAGRDGFIDLMELKLMMEKLGAP.QTHLGLK.MIKEVDEDFDSKLSF.EFLLIF.KAAA.EL.EDS.LC | |
| Retrocopy | YDAGRDGFIDLMELKLMMEKLGAP>QTHLGLKSMIKEVDEDFDSKLSFQEFLLIF*KAAARELEEDSALC |
| Parental | VLARLSEIDVSSEGVKGAKSFFEAKVQAINVSSRFEEEIKAEQEERKKQAEEMKQRKAAFKELQSTFK |
| VLA.LSEI...SEG..GAK.FFEAKVQAINVSSRF.EEIK.EQEERK....EMKQRKAAFKELQSTFK | |
| Retrocopy | VLAHLSEINIPSEGIEGAKTFFEAKVQAINVSSRFKEEIKSEQEERKH--AEMKQRKAAFKELQSTFK |
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 .22 RPM | 8 .65 RPM |
| SRP051959_heart | 0 .18 RPM | 1 .68 RPM |
| SRP051959_kidney | 0 .02 RPM | 12 .38 RPM |
| SRP051959_liver | 0 .06 RPM | 5 .61 RPM |
| SRP051959_lung | 0 .33 RPM | 14 .01 RPM |
| SRP051959_lymph_node | 0 .48 RPM | 9 .41 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .86 RPM |
| SRP051959_spleen | 0 .32 RPM | 15 .25 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3949 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3949 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3949 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000008888 | 1 retrocopy |
retro_cjac_3949 ,
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