RetrogeneDB ID: retro_ocun_1672

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018754:1734860..1735404(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AEBP2
• Ensembl ID: ENSOCUG00000016677
• Aliases: None
• Description: AE binding protein 2 [Source:HGNC Symbol;Acc:24051]

Sequence

>retro_ocun_1672
AGCATAAGCAGTACTATACTAGAGGTAGACAGCACAATTTCTAGTGGGCGTTTGACTCCGGCAATGATGAATGGACAAGG
AAGCATTACTTCTTCAAGCAAAAATATTGCCTAGAATCGTTGTTGGGACCAGTGGCCAGGCTTGCTCCAGCTCTAGGCCA
GATCTGGCAGATCATATCCCTTCCATACATGTAGATGGTCAGCAAGGAGGGGTATTTGTTTGCTTATGAAAAGGTTGTAA
AGTATCTAACACTCCATCAACCAGTCAAAGTTAGCTGCAGAGGCACATGCTGACGCACAGTGGAGACAAACCTTTCCAGT
GTGTTGTTGGCGGCTGCAATGCCAGCTTTGCTTCTCAGGGAGGGATAGTTCGCCATGTACCCACACACTTCAGTCAGCAG
AACCCCTCCAAAGTTTCTAGCCAGCCAAAGTCCAAAGAAGAATCTCCTTCTAAAGCTGAAATGAACAAAAGGAGGAAATT
AAAGAACAGAAGACAACGCTCATTACCGCGACCACATGATTTCTTCGATGCAAAAACACTGGAT

Alignment

ORF - retro_ocun_1672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.26 %
• Parental protein coverage: 61.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQC-QACFNSSPDLADHIRSIHVDGQRG
          SISSTI..VDSTISSGR.TPAMMNGQGS.TSSSKNIA.N.CWDQ..QAC..S.PDLADHI.SIHVDGQ.G
Retrocopy SISSTILEVDSTISSGRLTPAMMNGQGSITSSSKNIA*NRCWDQW>QACSSSRPDLADHIPSIHVDGQQG

Parental  GVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQQNSSKVS
          GVFVCL.KGCKV.NTPSTSQS.LQRHMLTHSGDKPF.CVVGGCNASFASQGG..RHVPTHFSQQN.SKVS
Retrocopy GVFVCL*KGCKVSNTPSTSQS*LQRHMLTHSGDKPFQCVVGGCNASFASQGGIVRHVPTHFSQQNPSKVS

Parental  SQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHDFFDAQTLD
          SQPK.KEESPSKA.MNKRRKLKN.R.RSLPRPHDFFDA.TLD
Retrocopy SQPKSKEESPSKAEMNKRRKLKNRRQRSLPRPHDFFDAKTLD

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	14.51 RPM
SRP017611_kidney	0.00 RPM	8.92 RPM
SRP017611_liver	0.00 RPM	4.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1672 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1672 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
Cavia porcellus	ENSCPOG00000007440	1 retrocopy	retro_cpor_431,
Myotis lucifugus	ENSMLUG00000006293	1 retrocopy	retro_mluc_1637,
Oryctolagus cuniculus	ENSOCUG00000016677	2 retrocopies	retro_ocun_1207, retro_ocun_1672 ,
Rattus norvegicus	ENSRNOG00000008929	1 retrocopy	retro_rnor_875,