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 symbol: CTSA
• Ensembl ID: ENSAPLG00000013472
• Aliases: None
• Description: cathepsin A [Source:HGNC Symbol;Acc:9251]

Sequence

>retro_apla_9
GGAATCACTGTGGGAAACAGCCTCTCCTCCTAGGAGATCAACAACAACTCACTAATTTACTTTGCCTATTACCACGGCCT
GCTGAGGACCCAGCTGTGGAAGGACTTATAGGCCTTCTCCCAGGGGAAGTGGAACTTCCATGATAACCCCAACCTTAACT
GCACACTCCAGATGGAGGAGATGATTCAGATTGTAGAGGACTCTGGCCTCAACATCTACAATCTCTACACCCCATGTGCT
GGCAGTGTCCCTGGAAGCATGAGGTGTGAGGGTGACTATCTCATCACACACAACATGGGAAACTCTTTCATCCATATGCC
GATGAGGTTCTTTTGGACACAGAACCTATTCTGGATGCCTGTAGCCTGGAAGAAGGTCCGGATGGACCTGCCGTGCACCA
ACTCCACAGTCCCTACCATGTATTTGAATTCCCTGGAGATGAGGAAGGGTTTTCACATGTTCCCTGATGCCCTGGAGTGG
CAGGAGTGCAGCTTTGAGGTGAACCGCAGCTACAAGTGCCTGTACATGCAGATGAATGACCAGTACCTGAAGCTGCTCGG
AGCCATGAAATACTGGATCCTGGTGTGCAATGGGGATGTCAACATGGTCTGCAACTTCCTTGGGGATGAGTGGTTTGTGG
ACTCCCTGTGCTAGAAGGTG

Alignment

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

Expression

RNA-Seq

Anas platyrhynchos was not studied using RNA-Seq expression data.

ChIP-Seq

Anas platyrhynchos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_apla_9 retrocopy.

TSS

Anas platyrhynchos was not studied using FANTOM5 data.

Lab

retro_apla_9 was not experimentally validated.

Homology

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 ,