RetrogeneDB ID: retro_ocun_1500

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:29551530..29551945(-)
• Located in intron of: ENSOCUG00000002826

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC43
• Ensembl ID: ENSOCUG00000017526
• Aliases: None
• Description: coiled-coil domain containing 43 [Source:HGNC Symbol;Acc:26472]

Sequence

>retro_ocun_1500
CTAGAAGGACAGTTAGAGTCGCTGGGAGCGGACTGAGCCATGTATTGCGTCCACATCCTTGGTGTCTTGCAGGAGAAGGA
GGAAGAGGAGAAGCTGGATACTCTACAGGGCATCTTGCGGGCTTTCCTGGAAGAAGATCTCTCTTAATGTCTGCAAGGAA
ATTGTAGATCGATGGTCAAATTTTCAAGTGTTGTTACCAGAGTGAAAAAGACAAGATGAGGTCTGGGCTATTGCCACCCT
CACTGAGAAGCCCACACAGTTGGTGTTGTCGCCCGGGATGGGGTCAGCAGAATAGAAGCAGAGGAAGGCTGCCCTCCTGG
CCCAGTACATGGATGTGACAGATGAAGAGGATGACCCAGGTGCCACCACAGTGAGCACTGGGTCTGATAGATCTCTGTAC
CCAGACACCAGCGTG

Alignment

ORF - retro_ocun_1500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.86 %
• Parental protein coverage: 55.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDGRLEALGVDQAVYGAYILGVLQEEEEEEKLDALQGILSAFLEEDSL-LDVCKEIVERWSESQSVVSKV
          L.G.LE.LG.D.A.Y...ILGVLQE.EEEEKLD.LQGIL.AFL.E..L.L.VCKEIV.RWS..Q......
Retrocopy LEGQLESLGAD*AMYCVHILGVLQEKEEEEKLDTLQGILRAFL-EEDL>LNVCKEIVDRWSNFQVLLPE*

Parental  EKEDEVQAIATLIEKQAQIVVKPRMVSEEAKQRKAALLAQYADVTDEETDADEKEDSGATSVNIGSDRSL
          ...DEV.AIATL.EK..Q.V..P.M.S.E.KQRKAALLAQY.DVTDEE.D......S.........D.S.
Retrocopy KRQDEVWAIATLTEKPTQLVLSPGMGSAE*KQRKAALLAQYMDVTDEEDDPGATTVSTGSDRSLYPDTSV

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	7.56 RPM
SRP017611_kidney	0.00 RPM	6.08 RPM
SRP017611_liver	0.00 RPM	2.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1500 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1500 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018379	1 retrocopy	retro_amel_1479,
Canis familiaris	ENSCAFG00000014115	1 retrocopy	retro_cfam_456,
Monodelphis domestica	ENSMODG00000011411	1 retrocopy	retro_mdom_1378,
Mustela putorius furo	ENSMPUG00000009224	1 retrocopy	retro_mputfur_1511,
Oryctolagus cuniculus	ENSOCUG00000017526	1 retrocopy	retro_ocun_1500 ,
Ochotona princeps	ENSOPRG00000006793	2 retrocopies	retro_opri_263, retro_opri_699,
Rattus norvegicus	ENSRNOG00000002748	1 retrocopy	retro_rnor_2906,
Sus scrofa	ENSSSCG00000017352	2 retrocopies	retro_sscr_173, retro_sscr_944,