RetrogeneDB ID: | retro_ptro_2171 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 5:98001146..98001746(+) | ||
| 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: | ENSPTRG00000014829 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_2171
ATGGTGCTGGTCCCCACCCACCACTTCAGAGACTTTGAGAGGAAACCAGAGTACCCATAGCTGGAGATGCCTGTCCGACC
TCCCTACCGTGGTCCTATGAGAACCATGTGGCTTATCCACGATGGCTGTGGCATCGCCTGTGCCATCATCACCTGGTTTC
TGGTCCTCTGTGCGGAGTTTGTGGTCCTCTTTTTCATGCTGATTCCATCCCAAGACTATGCATACAGCACCATCAATGGA
ATTGTGTTCAACCTGCTGACTTTCTTGGCCCTGGCCTCCCACTGCCAGGCCATGCTGACAGAGACCGGAGCAGTGCCCAA
ATGAAATGCCACAAATAATTCATCCAGAGTTTACAGATGAAGCCCAGGCATGTGGTATACTCGTGTCCCAGTGCTGCAGC
CTCAAGCCTGACCGAACCTGCCGCTGCAGTGTTTGTAAGGGGTGCATTCGCAGGGTGGACCCCCACTGTCCCTGGGTCAA
CATCTGCATCAAAGAGAACAACCAGAAGTGCTTTGTCCTGTTTATCATGTGCACAGCTCTCATTTCCTTGCCTGCCCTCA
TCATGGTGGATTACACTTCCTGGATTGCTGTGAAGAAGAT
ORF - retro_ptro_2171 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.04 % |
| Parental protein coverage: | 61.47 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MMLIPTHHFRNIERKPEYLQPEKCVPPPYPGPVGTMWFIRDGCGIACAIVTWFLVLYAEFVVLFVMLIPS |
| M.L.PTHHFR..ERKPEY...E..V.PPY.GP..TMW.I.DGCGIACAI.TWFLVL.AEFVVLF.MLIPS | |
| Retrocopy | MVLVPTHHFRDFERKPEYP*LEMPVRPPYRGPMRTMWLIHDGCGIACAIITWFLVLCAEFVVLFFMLIPS |
| Parental | RDYVYSIINGIVFNLLAFLALASHCRAMLTDPGAVPKGNAT-KEFIESLQLKPGQVVYKCP-KCCSIKPD |
| .DY.YS.INGIVFNLL.FLALASHC.AMLT..GAVPK.NAT.K.FI.SLQ.KP..VVY.CP..CCS.KPD | |
| Retrocopy | QDYAYSTINGIVFNLLTFLALASHCQAMLTETGAVPK*NAT<K*FIQSLQMKPRHVVYSCP<QCCSLKPD |
| Parental | RAHHCSVCKRCIRKMDHHCPWVNNCVGENNQKYFVLFTMYIALISLHALIMV-GFHFLHCFEED |
| R...CSVCK.CIR..D.HCPWVN.C..ENNQK.FVLF.M..ALISL.ALIMV.G.HFL.C.EED | |
| Retrocopy | RTCRCSVCKGCIRRVDPHCPWVNICIKENNQKCFVLFIMCTALISLPALIMV<GLHFLDCCEED |
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 | 30 .44 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 53 .52 RPM |
| SRP007412_heart | 0 .00 RPM | 37 .92 RPM |
| SRP007412_kidney | 0 .03 RPM | 65 .14 RPM |
| SRP007412_liver | 0 .00 RPM | 44 .78 RPM |
| SRP007412_testis | 0 .11 RPM | 108 .86 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2171 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2171 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2171 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3221 |
| Gorilla gorilla | retro_ggor_2187 |
| Pongo abelii | retro_pabe_2668 |
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 | ENSPPYG00000013950 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000005695 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000014829 | 1 retrocopy |
retro_ptro_2171 ,
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