RetrogeneDB ID: | retro_acar_174 | ||
Retrocopy location | Organism: | Anole lizard (Anolis carolinensis) | |
| Coordinates: | GL343305.1:1329614..1330069(+) | ||
| Located in intron of: | ENSACAG00000014122 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GTF2F2 | ||
| Ensembl ID: | ENSACAG00000028333 | ||
| Aliases: | None | ||
| Description: | general transcription factor IIF, polypeptide 2, 30kDa [Source:HGNC Symbol;Acc:4653] |
Retrocopy-Parental alignment summary:
>retro_acar_174
AAAGAGAGCTCCTTAGAGGAACTATCACTGGAAGGAAGAGTGGCCCAGTGTGCAGGATGCCGGCCTGCAGCCAGTGAAAA
CGATGTCAAGTTGAAAAGGCTGCAAATGGAAGAATCTTCCAAACCTGTAAGCTGGATAATACAGTTGGATAAAGCTGTAA
CCAAAACTACAAACCTGTGGTAAACCATCAGTAAAATATTGAGTGTGAAAAGAAGAAAAAAGATGGAAAGCGAGCACAGG
CTGAAAAGCAACAAGTCCTGGGCATGCTTTTTTCAGCTTTTGAAAAGCATCAGTATTATAACATTAAAGATTTGGTTGAT
ATAACAAAACAGCCAGTGAGAGGCTTGAAAGAAATATGAAGAGAAATAGGCATCTACAATGTTAAAAGGATGCACAAAAA
CACCTGGGAACTTAAACCAGAATACCAACATTATCAAGGTGAAGATAAACATGAT
ORF - retro_acar_174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.52 % |
| Parental protein coverage: | 66.23 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | ESSNTEKLSLEGIVVQRAECRPAASENYMKLKRLQIEESSKPVSWTMQLEKAVTT-NYKPVANHQYNIEY |
| ..S..E.LSLEG.V.Q.A.CRPAASEN..KLKRLQ.EESSKPVSW..QL.KAVT..NYKPV.NHQ.NIE. | |
| Retrocopy | KESSLEELSLEGRVAQCAGCRPAASENDVKLKRLQMEESSKPVSWIIQLDKAVTK<NYKPVVNHQ*NIEC |
| Parental | EKKKKEDGKRARAEKQQVLDMLFSAFEKHQYYNIKDLVDITKQPVSYLKEILREIGIYNVKGTHKNTWEL |
| EKKKK.DGKRA.AEKQQVL.MLFSAFEKHQYYNIKDLVDITKQPV..LKEI.REIGIYNVK..HKNTWEL | |
| Retrocopy | EKKKK-DGKRAQAEKQQVLGMLFSAFEKHQYYNIKDLVDITKQPVRGLKEI*REIGIYNVKRMHKNTWEL |
| Parental | KPEYRHYQGEDKSD |
| KPEY.HYQGEDK.D | |
| Retrocopy | KPEYQHYQGEDKHD |
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 |
|---|---|---|
| SRP009831_adrenal | 0 .00 RPM | 18 .51 RPM |
| SRP009831_brain | 0 .00 RPM | 43 .74 RPM |
| SRP009831_dewlap | 0 .00 RPM | 46 .57 RPM |
| SRP009831_embryo | 0 .03 RPM | 39 .30 RPM |
| SRP009831_heart | 0 .00 RPM | 15 .88 RPM |
| SRP009831_liver | 0 .08 RPM | 13 .70 RPM |
| SRP009831_lung | 0 .00 RPM | 16 .98 RPM |
| SRP009831_ovary | 0 .00 RPM | 37 .22 RPM |
| SRP009831_skeletal_muscle | 0 .00 RPM | 8 .52 RPM |
Anolis carolinensis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_acar_174 retrocopy.
Anolis carolinensis was not studied using FANTOM5 data.
retro_acar_174 was not experimentally validated.