RetrogeneDB ID: | retro_pabe_2668 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 5:98461841..98462442(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZDHHC3 | ||
| Ensembl ID: | ENSPPYG00000013950 | ||
| Aliases: | None | ||
| Description: | zinc finger, DHHC-type containing 3 [Source:HGNC Symbol;Acc:18470] |
Retrocopy-Parental alignment summary:
>retro_pabe_2668
ATGATGCTGGTCCCCGCCCACCGCTTCAGAGACTTTGAGAGGAAAACAGAGTACCCATAGCTGGAGATGCCTGTCTGACC
TCCCTACCCTGGTCCCGTGAGAACCATGTGATTTATCCACAAGGGCTGTGGCATTGCCTATGCCATCATCACCTGGTTTC
TGGTCCTCTATGCAGAGTTTGTGGTCCTCTTTTTCATGCTGATTCCATCCTGAGACTATGCATACAGCACCATCAATGGA
ATTATGTTCAACCTGCTGACTTTCTTGGCCCTGGCCTCCCACTGCCAGGCCATGCTGACAGACACCAGAGCAGTGCTTAA
ATGAAATGCCACTAAATAATTCATCCCGAGTTTACAGATGAAGCCCAGGCATGTGGTGTACTCATGTCCCAGTGCTGCAG
GATCAAGCCTGACTGAGCCTGCCGCCACAGTGTTTGTAAGAGGTGCATTTGCAGGGTGGAACCCCACTGTCCCTGGGTCA
ACATCTGCATCGAAGAGAACAACCAGAATTGCTTTGTCCTGTTTATCATGTGCACAGCTCTCATTTCCTTACCTGCCCTC
ACTGTGGTGGATTCCACTTCCTGGATTGCTGTGAAGAAGAT
ORF - retro_pabe_2668 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.44 % |
| Parental protein coverage: | 61.47 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MMLIPTHHFRDIERKPEYLQPEKCVPPPYPGPVGTMWFIRDGCGIACAIVTWFLVLYAEFVVLFVMLIPS |
| MML.P.H.FRD.ERK.EY...E..V.PPYPGPV.TM.FI..GCGIA.AI.TWFLVLYAEFVVLF.MLIPS | |
| Retrocopy | MMLVPAHRFRDFERKTEYP*LEMPV*PPYPGPVRTM*FIHKGCGIAYAIITWFLVLYAEFVVLFFMLIPS |
| Parental | RDYVYSIINGIVFNLLAFLALASHCRAMLTDPGAVPKGNATKEFIESLQLKPGQVVYKCP-KCCSIKPDR |
| .DY.YS.INGI.FNLL.FLALASHC.AMLTD..AV.K.NATK.FI.SLQ.KP..VVY.CP..CC.IKPD. | |
| Retrocopy | *DYAYSTINGIMFNLLTFLALASHCQAMLTDTRAVLK*NATK*FIPSLQMKPRHVVYSCP<QCCRIKPD* |
| Parental | AHHCSVCKRCIRKMDHHCPWVNNCVGENNQKYFVLFTMYIALISLHALIMV-GFHFLHCFEED |
| A...SVCKRCI.....HCPWVN.C..ENNQ..FVLF.M..ALISL.AL..V.GFHFL.C.EED | |
| Retrocopy | ACRHSVCKRCICRVEPHCPWVNICIEENNQNCFVLFIMCTALISLPALTVV<GFHFLDCCEED |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 40 .14 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 35 .39 RPM |
| SRP007412_heart | 0 .00 RPM | 14 .69 RPM |
| SRP007412_kidney | 0 .00 RPM | 26 .58 RPM |
| SRP007412_liver | 0 .00 RPM | 12 .12 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2668 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2668 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2668 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3221 |
| Pan troglodytes | retro_ptro_2171 |
| Gorilla gorilla | retro_ggor_2187 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000163812 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000005201 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000013950 | 1 retrocopy |
retro_pabe_2668 ,
|
| Pan troglodytes | ENSPTRG00000014829 | 1 retrocopy |