RetrogeneDB ID: | retro_apla_9 | ||
Retrocopy location | Organism: | Duck (Anas platyrhynchos) | |
| Coordinates: | KB742388.1:861113..861773(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSAPLG00000005363 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CTSA | ||
| Ensembl ID: | ENSAPLG00000013472 | ||
| Aliases: | None | ||
| Description: | cathepsin A [Source:HGNC Symbol;Acc:9251] |
Retrocopy-Parental alignment summary:
>retro_apla_9
GGAATCACTGTGGGAAACAGCCTCTCCTCCTAGGAGATCAACAACAACTCACTAATTTACTTTGCCTATTACCACGGCCT
GCTGAGGACCCAGCTGTGGAAGGACTTATAGGCCTTCTCCCAGGGGAAGTGGAACTTCCATGATAACCCCAACCTTAACT
GCACACTCCAGATGGAGGAGATGATTCAGATTGTAGAGGACTCTGGCCTCAACATCTACAATCTCTACACCCCATGTGCT
GGCAGTGTCCCTGGAAGCATGAGGTGTGAGGGTGACTATCTCATCACACACAACATGGGAAACTCTTTCATCCATATGCC
GATGAGGTTCTTTTGGACACAGAACCTATTCTGGATGCCTGTAGCCTGGAAGAAGGTCCGGATGGACCTGCCGTGCACCA
ACTCCACAGTCCCTACCATGTATTTGAATTCCCTGGAGATGAGGAAGGGTTTTCACATGTTCCCTGATGCCCTGGAGTGG
CAGGAGTGCAGCTTTGAGGTGAACCGCAGCTACAAGTGCCTGTACATGCAGATGAATGACCAGTACCTGAAGCTGCTCGG
AGCCATGAAATACTGGATCCTGGTGTGCAATGGGGATGTCAACATGGTCTGCAACTTCCTTGGGGATGAGTGGTTTGTGG
ACTCCCTGTGCTAGAAGGTG
ORF - retro_apla_9 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.28 % |
| Parental protein coverage: | 64.35 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GIAVGNGLSSYEINDNSLVYFAYYHGLLGTQLWKDLQTFCCSQGKCNFHDNSNLNCTLKMEEMIQIVEES |
| GI.VGN.LSS.EIN.NSL.YFAYYHGLL.TQLWKDL..F..SQGK.NFHDN.NLNCTL.MEEMIQIVE.S | |
| Retrocopy | GITVGNSLSS*EINNNSLIYFAYYHGLLRTQLWKDL*AF--SQGKWNFHDNPNLNCTLQMEEMIQIVEDS |
| Parental | GLNIYNLYAPCAGGVPGSMRYEGDYLVTHDLGNSFIRMPLKFSWRQNLFRMPVARKKVRMDPPCTNSTAP |
| GLNIYNLY.PCAG.VPGSMR.EGDYL.TH..GNSFI.MP..F.W.QNLF.MPVA.KKVRMD.PCTNST.P | |
| Retrocopy | GLNIYNLYTPCAGSVPGSMRCEGDYLITHNMGNSFIHMPMRFFWTQNLFWMPVAWKKVRMDLPCTNSTVP |
| Parental | TMYLNSPEVRKALHIPPEAPEWQVCSFEVNRSYKRLYMQMNEQYLKLLGAGKYRILVYNGDVDMACNFLG |
| TMYLNS.E.RK..H..P.A.EWQ.CSFEVNRSYK.LYMQMN.QYLKLLGA.KY.ILV.NGDV.M.CNFLG | |
| Retrocopy | TMYLNSLEMRKGFHMFPDALEWQECSFEVNRSYKCLYMQMNDQYLKLLGAMKYWILVCNGDVNMVCNFLG |
| Parental | DEWFVDSLCQKV |
| DEWFVDSLC.KV | |
| Retrocopy | DEWFVDSLC*KV |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Anas platyrhynchos was not studied using RNA-Seq expression data.
Anas platyrhynchos was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_apla_9 retrocopy.
Anas platyrhynchos was not studied using FANTOM5 data.
retro_apla_9 was not experimentally validated.
Retrocopy orthology:
Anas platyrhynchos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anas platyrhynchos | ENSAPLG00000013472 | 1 retrocopy |
retro_apla_9 ,
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