RetrogeneDB ID: | retro_pabe_2143 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 2b:94453630..94454357(-) | ||
| Located in intron of: | ENSPPYG00000013091 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZNF670 | ||
| Ensembl ID: | ENSPPYG00000000040 | ||
| Aliases: | None | ||
| Description: | zinc finger protein 670 [Source:HGNC Symbol;Acc:28167] |
Retrocopy-Parental alignment summary:
>retro_pabe_2143
GTGACTTTTGAGGATGTGGCTGTAACCTTCACCCCCTCAGGAGTGGGCGTTGCTGGATTTTTCCCAGAAGAAACTCTTAT
AGAGATGTGACGCAGGAAACCTTCAGGAATTTGGTTTCTACAGGAAACAAATGGGAAGACCAGAATGTTGATGATCAAGT
CAGAAAATATGGGAGAAATGTAAGTCATATGGTAGAGAGACTGTGTGAAGGTAAACAAAATAGTCAAGGTGGAGAAACCT
TCAGCCAGAATTCAAATCTTAATCTAGAACAAGAAAGTTTCTACTAAAGTAAAACCATGTGTATGCAGAATTGTGTGGAA
AAGTCTTCATATGTCATGCATCTCTTCACAGGTATATTATATCTCACTCTGGACACAAACTATTTGAGTGTGAGGACTGT
GAAATGAAGCCATATAAATGTAAACAATAATGAGAAAGCCTTTAATTCTCTCACAGGTGTTTGAAGACACATGGTAATGC
ACAGTGATAACGGATTTTATAAATGTACAGTATGTGGGGAAAACTTTATTTTCCCCAGTTTATTTCAAATGCACCAGAAA
ACTCACACTGGAGAAAACAACCCTATAAATGTAAACATTGTGGTAAAGACTTCAATATTCCAGAAACTGTCACGAACATG
AAATAACTCATAGTGGAGAGAAACCCTATGCATGCAATAAAAAATGATAAATTATTAGCTTCTTCCTACACCCTTCGAGA
ACATGAA
ORF - retro_pabe_2143 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.0 % |
| Parental protein coverage: | 62.11 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 9 |
Retrocopy - Parental Gene Alignment:
| Parental | VSFEDVAVAFTQ-EEWALLDPSQKNL-YRDVMQEIFRNLASVGNKSEDQNIQDDFKNPGRNLSSHVVERL |
| V.FEDVAV.FT...EWALLD.SQK.L.YRDV.QE.FRNL.S.GNK.EDQN..D.....GRN.S.H.VERL | |
| Retrocopy | VTFEDVAVTFTP>QEWALLDFSQKKL>YRDVTQETFRNLVSTGNKWEDQNVDDQVRKYGRNVS-HMVERL |
| Parental | FAIKEGSQYGETFSQDSNLNL-NKKVSTGVKPCECSV-CGKVFICHSALHRHILSHTGNKLFECEECPEK |
| ...K..SQ.GETFSQ.SNLNL.NKKVST.VKPC.C...CGKVFICH..LHR.I.SH.G.KLFECE.C..K | |
| Retrocopy | CEGKQNSQGGETFSQNSNLNL>NKKVSTKVKPCVCRI>CGKVFICHASLHRYIISHSGHKLFECEDCEMK |
| Parental | LYHCKQ-CGRAFISLTSVDRHMVTHSSNGPYKGPVYEKPFDF-PSVFQM-PQSTYTGEKTYKCKHCDKAF |
| .Y.CKQ....AF.SLT.V.RHMV.HS.NG.YK..V....F.F.P..F...P.........YKCKHC.K.F | |
| Retrocopy | PYKCKQ>NEKAFNSLTGV*RHMVMHSDNGFYKCTVCGENFIF>PVYFKC>PENSHWRKQPYKCKHCGKDF |
| Parental | S-YSSYLREHERTHTGEKPYACK-KCGKSFTFSSSLRQHE |
| ..YS....EHE.TH.GEKPYAC..K..K....S..LR.HE | |
| Retrocopy | N<YSRNCHEHEITHSGEKPYACN>KNDKLLASSYTLREHE |
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 | 0 .22 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .19 RPM |
| SRP007412_heart | 0 .06 RPM | 0 .33 RPM |
| SRP007412_kidney | 0 .07 RPM | 0 .66 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .55 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2143 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2143 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2143 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000135747 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000000040 | 1 retrocopy |
retro_pabe_2143 ,
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