RetrogeneDB ID: retro_ocun_897

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:46236782..46237865(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000002503
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ASH2L
• Ensembl ID: ENSOCUG00000029521
• Aliases: None
• Description: ash2 (absent, small, or homeotic)-like (Drosophila) [Source:HGNC Symbol;Acc:744]

Sequence

>retro_ocun_897
CAGAGACCTGGGAAAATGACTTGGCCAAAAAACATTGTTAAAACCATTAGTAAAGAGAGAGATGTGTTTTTGGTAAAGGA
GCACCCTGATCCAGGGAGCAAAGACCCTGAAGATTACCCCAAATTTGGACTTCTGAATCAGGATCTTAGTAACATCGGTC
CTGCTTACAACAACCAGAAACAAAGCAGTGCTGTGTCTACCAGTGGGAATCTAAATGGGGGCATTGCAGCAGGGAGCAGT
GGAAAAGGAAGAGGAGCCAAGCACAAACAGCAGGATGGAGGGACCACGGGGACCACCAAGAAGGCCCGCAGTGACCCTTT
GTTTTCTGTTCAGCACCTTCCCCCTCATGGCTACCCCTTGGAGCATCCATTTAATAAAGATGGCTATCGGTATATTTTAG
CTGAGCCTGACCCCCATGCCCCTGACCCTGAGAAGCTCGAACTTGACTGTTGGGCAGGAAAATCTATCCCTGGAGACCTC
TACAGAGCCTGCTTGTACGAGCGAGTTTTGTTAGCCCTACATGATAGAGCTCCCCAGCTGAAGATCTTCAATGACCGGCT
GACTGTGGTTGGAGAGAAGGGCTACTCCATGGTGGGGGCCTCTCATGGGGTATGGAAAGGTGCCTGGTACTTTGAGATCA
CTGTGAATGAGATGCCACCCGACACTGCTGCCAGACTGGGTTGGTCTCAGCCCTTAGGCAACCTCCAAGCTCCCTTGGGC
TATGATAAATTCAGCTATCCTTGGCGGAGCAAAAAGGGAACCAAGTTCCATCAGTCCATTGGCAAACACTACTCCTCTGG
CTACGGACAGGGAGATGTCCTGGGATTCTACATCAACCTTCCTGAAGACACGGAGACAGGCAAGTCATTGCCTGACACAT
ACAAAGACAAGGCTTTGATCAAGTTCAAGAGTTATCTGTATTTTGAGGAGAAAGACTTCGTGGATAAAGCAGAGAAGTGC
CTAAAGCGGAGTCCCCATAGTGAGATAATATTTTATAAAAATGGTGCCAATCAAAGTGTGGCTTACAAAGATATTTTTGA
GGGGGTTTACTTCCCAGCCATCTCACTGTACAAAAGCTGCACA

Alignment

ORF - retro_ocun_897 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.76 %
• Parental protein coverage: 97.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRPGKMTWPNNIVKTMSKERDVFLVKEHPDPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQSSAVSTSG
          QRPGKMTWP.NIVKT.SKERDVFLVKEHPDPGSKDPE.DYPKFGLL.QDLSNIGPAY.NQKQSSAVSTSG
Retrocopy QRPGKMTWPKNIVKTISKERDVFLVKEHPDPGSKDPE-DYPKFGLLNQDLSNIGPAYNNQKQSSAVSTSG

Parental  NLNGGAILGGGIAAGSSGKGRGAKRKQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEHPFNKDGYRYIL
          NLNGG...G........G.G..AK.KQQDGGTTGTTKKARSDPLFS.Q.LPPHGYPLEHPFNKDGYRYIL
Retrocopy NLNGGIAAG----SSGKGRG--AKHKQQDGGTTGTTKKARSDPLFSVQHLPPHGYPLEHPFNKDGYRYIL

Parental  AEPDPHAPDPEKLELDCWAGKPIPGDLYRACLYERVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHG
          AEPDPHAPDPEKLELDCWAGK.IPGDLYRACLYERVLLALHDRAPQLKI..DRLTVVGEKGYSMV.ASHG
Retrocopy AEPDPHAPDPEKLELDCWAGKSIPGDLYRACLYERVLLALHDRAPQLKIFNDRLTVVGEKGYSMVGASHG

Parental  VRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDV
          V.KGAWYFEITV.EMPPDTAARLGWSQPLGNLQAPLGYDKFSY.WRSKKGTKFHQSIGKHYSSGYGQGDV
Retrocopy VWKGAWYFEITVNEMPPDTAARLGWSQPLGNLQAPLGYDKFSYPWRSKKGTKFHQSIGKHYSSGYGQGDV

Parental  LGFYINLPEDTETAKSLPDTYKDKALIKFKSYLYFEEKDFVDKAEKSLKQTPHSEIIFYKNGANQGVAYK
          LGFYINLPEDTET.KSLPDTYKDKALIKFKSYLYFEEKDFVDKAEK.LK..PHSEIIFYKNGANQ.VAYK
Retrocopy LGFYINLPEDTETGKSLPDTYKDKALIKFKSYLYFEEKDFVDKAEKCLKRSPHSEIIFYKNGANQSVAYK

Parental  DIFEGVYFPAISLYKSCT
          DIFEGVYFPAISLYKSCT
Retrocopy DIFEGVYFPAISLYKSCT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	3.04 RPM	28.75 RPM
SRP017611_kidney	1.93 RPM	11.96 RPM
SRP017611_liver	0.54 RPM	4.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_897 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_897 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_897 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000029521	2 retrocopies	retro_ocun_872, retro_ocun_897 ,
Sorex araneus	ENSSARG00000002606	1 retrocopy	retro_sara_80,