RetrogeneDB ID: retro_ocun_335

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:10020215..10020477(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INIP
• Ensembl ID: ENSOCUG00000016717
• Aliases: None
• Description: INTS3 and NABP interacting protein [Source:HGNC Symbol;Acc:24994]

Sequence

>retro_ocun_335
ATGGCAGCAAACCCTTCGGGACAAGGTTTTCAGAACAAAAACAGAGTTGCAATCTTGGCAGAACTGGACAAAGAGAAAAG
AAAATTGCTTATGCAGAACCAGTCTTCAACAAATCATGCTGGAGCTGGCATCGCGCTCTGGAGGCCGGCTCTCAACAAGG
ACTCCGCGATCTCGCTGAGCAGCAGCACCTCGCCGCCGTGCAGCAGAAGGCAGCCTGCAGCATGCTCACGCACATTCATC
TGGATACTTCATAACTCAAGAC

Alignment

ORF - retro_ocun_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 83.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAANPSGQGFQNKNRVAILAELDKEKRKLLMQNQSSTNHPGAGIALSRPALSKD-FRDHAEQQHIAA-QQ
          MAANPSGQGFQNKNRVAILAELDKEKRKLLMQNQSSTNH.GAGIAL.RPAL.KD..RD.AEQQH.AA.QQ
Retrocopy MAANPSGQGFQNKNRVAILAELDKEKRKLLMQNQSSTNHAGAGIALWRPALNKD<LRDLAEQQHLAAVQQ

Parental  KAA-LQHAHAHSSGYFITQD
          KAA.LQHAHAHSSGYFITQD
Retrocopy KAA<LQHAHAHSSGYFITQD

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	8.11 RPM
SRP017611_kidney	0.00 RPM	6.08 RPM
SRP017611_liver	0.00 RPM	1.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_335 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_335 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006841	1 retrocopy	retro_amel_1661,
Equus caballus	ENSECAG00000008524	1 retrocopy	retro_ecab_187,
Homo sapiens	ENSG00000148153	1 retrocopy	retro_hsap_2980,
Microcebus murinus	ENSMICG00000001130	1 retrocopy	retro_mmur_92,
Nomascus leucogenys	ENSNLEG00000016554	1 retrocopy	retro_nleu_1508,
Oryctolagus cuniculus	ENSOCUG00000016717	1 retrocopy	retro_ocun_335 ,
Oryzias latipes	ENSORLG00000011577	1 retrocopy	retro_olat_8,
Pan troglodytes	ENSPTRG00000023472	1 retrocopy	retro_ptro_2015,
Sorex araneus	ENSSARG00000003661	1 retrocopy	retro_sara_104,
Xiphophorus maculatus	ENSXMAG00000002259	1 retrocopy	retro_xmac_8,