RetrogeneDB ID: retro_ocun_1871

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:7619520..7620027(+)
• Located in intron of: ENSOCUG00000016386

Retrocopy information

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

Parental gene information

• Parental gene symbol: YY2
• Ensembl ID: ENSOCUG00000026938
• Aliases: None
• Description: YY2 transcription factor [Source:HGNC Symbol;Acc:31684]

Sequence

>retro_ocun_1871
GATGGTTCAAGTTCTGATTATTCTGAGTACTTCACAGGGAAGAAACTTCCTCCTGGAGGAATACCTGTTGTTGACCTCTC
AGACCCCAAACAGCTTGCCGAATTTGCCAAAATGAAGCCGAGAAAACCCCAGGACAGTAGTTCGAGGACGGTAGCTTGCC
CTCATAAAGACTGTGAAAAGATGTTCAGGGATAACTGTGCCATGAGAAAACATCTGCACACCCACGGTCCCAGGGTCCAC
GTGTGCACAGAGTGCGGCAAAGCTTTTATTGAGAACTCGAAGCTAAAACGACATCAACTGGTTCACACTGGAGAGAAGCC
CTTTCAGTGCACGTTCGAAGGCTGCGGAAAACGCTTTTCCCTGGATTTCAATTTGCGCACCCATGTGCGAATCCACACCG
GAGATAAGCCGTTTGTTTGCCCTTATGATGCCTGTAATAAGAAGTTCGCTCAGTCAACTAACCTGAAGTCACACATCTTA
ACGCATGCTAAGAACAAAGCCAGCCAG

Alignment

ORF - retro_ocun_1871 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.53 %
• Parental protein coverage: 73.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHKGCTKMFRDNSAMR
          ..S..DYSEY.TGKKLPPGGIP..DLSDPKQLAEFA.MKPRK...D...RT.ACPHK.C.KMFRDN.AMR
Retrocopy DGSSSDYSEYFTGKKLPPGGIPVVDLSDPKQLAEFAKMKPRK-PQDSSSRTVACPHKDCEKMFRDNCAMR

Parental  KHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYV
          KHLHTHGPRVHVC.ECGKAF.E.SKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGD.P.V
Retrocopy KHLHTHGPRVHVCTECGKAFIENSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDKPFV

Parental  CPFDGCNKKFAQSTNLKSHILTHAKAKNNQ
          CP.D.CNKKFAQSTNLKSHILTHAK.K..Q
Retrocopy CPYDACNKKFAQSTNLKSHILTHAKNKASQ

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	0.22 RPM	21.96 RPM
SRP017611_kidney	0.00 RPM	28.38 RPM
SRP017611_liver	0.15 RPM	18.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1871 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1871 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Bos taurus	ENSBTAG00000020819	1 retrocopy	retro_btau_91,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Cavia porcellus	ENSCPOG00000020809	2 retrocopies	retro_cpor_1220, retro_cpor_1522,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mustela putorius furo	ENSMPUG00000002931	1 retrocopy	retro_mputfur_867,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871 ,