RetrogeneDB ID: retro_ocun_872

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:46591107..46592139(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_872
AGAGAGAGAGATGTGTTTTTGGTAAAGGAGCACCCTGATCCAGGGAGCAAAGACCCTGAAGATTACCCCAAATTTGGACT
TCTGAATCAGGATCTTAGTAACATCGGTCCTGCTTACAACAACCAGAAACAAAGCAGTGCTGTGTCTACCAGTGGGAATC
TAAATGGGGGCATTGCAGCAGGGAGCAGTGGAAAAGGAAGAGGAGACAAGCGCAAACAGCAGGATGGAGGGACCACGGGG
ACCACCAAGAAGGCCCGCAGTGACCCTTTATTTTCTGCTCAGCGCCTTCCCCCTCATGGCTACCCCTTGGAGCATCCATT
TAATAAAGATGGCTATCGGTATATTTTAGCTGAGCCTGACCCCCACGCCCCTGACCCTGAGAAGCTCGAACTTGACTGTT
GGGCAGGAAAACCTATCCCTGGAGACCTCTACAGAGTCTGCTTGTACGAGCGAGTTTTGTTAGCCCTACATGATAGAGCT
CCCCAGCTGAAGATCTCCAATGACCGGCTGACTGTGGTTGGAGAGAAGGGCTACTCCATGGTGCGGGCCTGTCACGGGGT
GTGGAAAGGTGCCTGTTACTTTGAGATCACTGTGGATGAGATGCCACCCGACACTGCTGCCAGACTGGGTTGGTCTCAGC
CCTTAGGCAACCTCCAAGCTCCCTTGGGCTATGATAAATTCAGCTGTTCTTGGTGGAGCAAAAAGGGAACCAAGTTCCAT
CAGTCCATTGGCAAACACTACTCTTCTGGCTACGGACAGGGAGATGTCCTGGGATTCTACATCAACCTTCCTGAAGACAG
GGAGACAGCCAAGTCATTGCCTGACACATACAAAGACAAGGCTTTGATCAAGTTCAAGAGTTTTCTGTATTTTGAGGAGA
AAGACTTCGTGGGTAAAGCAGAGAAGTGCCTAAAGCAGACTCCCCATAGTGAGATAATATTTTATAAAAATGCTGCCAAT
CAAGGTGTGGCTTACAAAGATATTTTTGAGGGGATTTACTTCCCAGCCATCTCACTGTATAAGAGCTGCACG

Alignment

ORF - retro_ocun_872 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.31 %
• Parental protein coverage: 93.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KERDVFLVKEHPDPGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQSSAVSTSGNLNGGAILGGGIAAGSS
          .ERDVFLVKEHPDPGSKDPE.DYPKFGLL.QDLSNIGPAY.NQKQSSAVSTSGNLNGG...G........
Retrocopy RERDVFLVKEHPDPGSKDPE-DYPKFGLLNQDLSNIGPAYNNQKQSSAVSTSGNLNGGIAAG----SSGK

Parental  GKGRGAKRKQQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLELDC
          G.G...K..QQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLELDC
Retrocopy GRGDKRK--QQDGGTTGTTKKARSDPLFSAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLELDC

Parental  WAGKPIPGDLYRACLYERVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPP
          WAGKPIPGDLYR.CLYERVLLALHDRAPQLKIS.DRLTVVGEKGYSMVRA.HGV.KGA.YFEITVDEMPP
Retrocopy WAGKPIPGDLYRVCLYERVLLALHDRAPQLKISNDRLTVVGEKGYSMVRACHGVWKGACYFEITVDEMPP

Parental  DTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTETAKSL
          DTAARLGWSQPLGNLQAPLGYDKFS.SW.SKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPED.ETAKSL
Retrocopy DTAARLGWSQPLGNLQAPLGYDKFSCSWWSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDRETAKSL

Parental  PDTYKDKALIKFKSYLYFEEKDFVDKAEKSLKQTPHSEIIFYKNGANQGVAYKDIFEGVYFPAISLYKSC
          PDTYKDKALIKFKS.LYFEEKDFV.KAEK.LKQTPHSEIIFYKN.ANQGVAYKDIFEG.YFPAISLYKSC
Retrocopy PDTYKDKALIKFKSFLYFEEKDFVGKAEKCLKQTPHSEIIFYKNAANQGVAYKDIFEGIYFPAISLYKSC

Parental  T
          T
Retrocopy T

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	3.37 RPM	28.75 RPM
SRP017611_kidney	1.42 RPM	11.96 RPM
SRP017611_liver	0.31 RPM	4.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_872 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_872 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_872 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,