RetrogeneDB ID: retro_ocun_514

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:82744296..82745606(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023745
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BYSL
• Ensembl ID: ENSOCUG00000017567
• Aliases: None
• Description: bystin-like [Source:HGNC Symbol;Acc:1157]

Sequence

>retro_ocun_514
ATGCCGAAATTCAAAGCGGCCCGTGGGGCTGGTGCTCAGGAAAAACACGCGCCCCTGGCAGAGCAGATCTTGGCTGGGAA
CGCGGTGCGGGCAAGTGCCCGGGAAAAGCGGCGGGGCCACGGAACCGGGGAAGAGGAGGAAGAGTATGTGGGGCCCCGGC
TGAGCCGGCGGATTTTGCAGCAAGCACGGCAACAACAGGAGGAGCTGGAAACCGAGCACGGCTCTGGGGACGGGCCCGCC
AAGCCTCGGGAGCGCGCCACGCGGCTGGGTCCTGGAGTGCCACAGGATGGGTCAGACGATGAGGATGAGAAGTGGCCCAC
CCTGGAGAAGGCTGCCACGATGAAGGGGGTAGACCACCATGCAGAGGTGGTCGTGGACCCTGAGGATGAGCGTGCCATTG
AGATGTTCATGAACAAGAACCCTCCTGCCAGGCGCACCCTGGCCGACATCATCATGGAGAAGCTGACTGAGAAGCAGACG
GAGGTCGAGACGGTCATGTCAGAGGTGTCAGGCTTCCCTATGCCCCAGCTGGACCCCCGGGTGCTGGAGGTCTACAGGGG
GGTCCGGGAGGTGTTGTCTAAGTACCGCAGCGGGAAACTGCCCAAGGCCTTTAAGATCATCCCTGCACTCTCCAACTGGG
AACAGATCCTCTATGTCACAGAGCCTGAGGCCTGGACTGCGGCCGCCATGTACCAAGCCACCAGGATTTTTGCTTCTAAC
CTGAAAGAACGCATGGCCCAGCGCTTCTACAACCTCGTCCTGCTCCCCCGCATACGAGATGACATCGCTGAATACAAACG
ACTCAACTTCCATTTGTACATGGCGCTCAAGAAGGCCTTGTTCAAGCCTGGAGCCTGGTTCAAAGGGATCCTGATCCCCC
TGTGCGAGTCAGGCCTTGTACTCTCCGGGAAGCCATCATCGTGGGCAGCATCATCACCAAGTGCTCTATCCCTGTGCTGC
ACTCCAGCGCGGCCAGGCTGAAAATCGCCGAGATGGAATACAGTGGTGCCAACAGCATCTTCCTACGACTGCTGCTGGAT
AAGAAGTACGCACTGCCCTACCGCGTGCTGGATGCCCTGGTCTTCCACTTCCTGGCGTTCCGGACAGAGAAGCGGGAGCT
GCCCGTGCTCCGGCACCAGTGCCTGCTGACATTGGTCCAGCGCTACAAGGCAGATTTGGCCACAGAACAGAAAGAAACCC
TCATGGAACTGCTCCGGCTGCAGCCCCACCCACAGCTGTCCCCCGAAATCAGGCGGGAGCTTCAGAGCGCAGTCCCTCGT
GACGTAGAAGATGTCCCCATCGCCATGGAG

Alignment

ORF - retro_ocun_514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.72 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKFKAARGAGAQEKHAPLAEQILAGNAVRSSAREKRRGRGTGEEEEEYVGPRLSRRILQQARQQQEELE
          MPKFKAARGAGAQEKHAPLAEQILAGNAVR.SAREKRRG.GTGEEEEEYVGPRLSRRILQQARQQQEELE
Retrocopy MPKFKAARGAGAQEKHAPLAEQILAGNAVRASAREKRRGHGTGEEEEEYVGPRLSRRILQQARQQQEELE

Parental  TEHGSGDGPAKPRERATRLGPGVPQDGSDDEDEEWPTLEKAATMKGVDHHAEVVVDPEDERAIEMFMNKN
          TEHGSGDGPAKPRERATRLGPGVPQDGSDDEDE.WPTLEKAATMKGVDHHAEVVVDPEDERAIEMFMNKN
Retrocopy TEHGSGDGPAKPRERATRLGPGVPQDGSDDEDEKWPTLEKAATMKGVDHHAEVVVDPEDERAIEMFMNKN

Parental  PPARRTLADIIMEKLTEKQTEVETVMSEVSGFPMPQLDPRVLEVYRGVREVLSKYRSGKLPKAFKIIPAL
          PPARRTLADIIMEKLTEKQTEVETVMSEVSGFPMPQLDPRVLEVYRGVREVLSKYRSGKLPKAFKIIPAL
Retrocopy PPARRTLADIIMEKLTEKQTEVETVMSEVSGFPMPQLDPRVLEVYRGVREVLSKYRSGKLPKAFKIIPAL

Parental  SNWEQILYVTEPEAWTAAAMYQATRIFASNLKERMAQRFYNLVLLPRIRDDIAEYKRLNFHLYMALKKAL
          SNWEQILYVTEPEAWTAAAMYQATRIFASNLKERMAQRFYNLVLLPRIRDDIAEYKRLNFHLYMALKKAL
Retrocopy SNWEQILYVTEPEAWTAAAMYQATRIFASNLKERMAQRFYNLVLLPRIRDDIAEYKRLNFHLYMALKKAL

Parental  FKPGAWFKGILIPLCESG-TCTLREAIIVGSIITKCSIPVLHSSAAMLKIAEMEYSGANSIFLRLLLDKK
          FKPGAWFKGILIPLCESG..CTLREAIIVGSIITKCSIPVLHSSAA.LKIAEMEYSGANSIFLRLLLDKK
Retrocopy FKPGAWFKGILIPLCESG<PCTLREAIIVGSIITKCSIPVLHSSAARLKIAEMEYSGANSIFLRLLLDKK

Parental  YALPYRVLDALVFHFLGFRTEKRELPVLWHQCLLTLVQRYKADLATEQKEALMELLRLQPHPQLSPEIRR
          YALPYRVLDALVFHFL.FRTEKRELPVL.HQCLLTLVQRYKADLATEQKE.LMELLRLQPHPQLSPEIRR
Retrocopy YALPYRVLDALVFHFLAFRTEKRELPVLRHQCLLTLVQRYKADLATEQKETLMELLRLQPHPQLSPEIRR

Parental  ELQSAVPRDVEDVPITME
          ELQSAVPRDVEDVPI.ME
Retrocopy ELQSAVPRDVEDVPIAME

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	0.00 RPM	9.38 RPM
SRP017611_kidney	0.10 RPM	5.98 RPM
SRP017611_liver	0.00 RPM	2.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_514 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_514 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_514 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010101	1 retrocopy	retro_btau_1246,
Choloepus hoffmanni	ENSCHOG00000011476	1 retrocopy	retro_chof_1615,
Macropus eugenii	ENSMEUG00000000759	2 retrocopies	retro_meug_1365, retro_meug_608,
Oryctolagus cuniculus	ENSOCUG00000017567	1 retrocopy	retro_ocun_514 ,