RetrogeneDB ID: retro_ocun_1642

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018737:595266..595662(-)
• Located in intron of: ENSOCUG00000012163

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMCO1
• Ensembl ID: ENSOCUG00000008441
• Aliases: None
• Description: transmembrane and coiled-coil domains 1 [Source:HGNC Symbol;Acc:18188]

Sequence

>retro_ocun_1642
ATGAGCACCACATTCGTGGACACTCTACTCATTGTTTCACCTCCGTGCGCACGGCTCTTCTCACTGAGGGCATTAACCTG
CGTCCTGGTGTACAGGACAGACAAGTACAAGAGGCTGAAGGCAGAAGCGGAAAAGCAGAGAGAGGAAGAAGGAAATGATG
ACAGAGTCAGCTGGTTGACAACAAAAAAGAAGAAAATAGAGAGGCAAGAAAAGAAACGGAAGACTAACAAGAGATCAATA
GCTCGAATGAAATCCATGTTTGCAATGGGCTTTTGTTTTCCTGCCCTAATGGGAACGTTCAATTCCATATTCAGTGGTCG
AGTTGTAGCAAAACTGTCTGACCCCTTTTCCTTCACCCAAGGACGGCCTCATCGACACCTGCTGGGGGGTGACACA

Alignment

ORF - retro_ocun_1642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.0 %
• Parental protein coverage: 73.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSTMFADTLLIV-FISVCTALLAEGI-TWVLVYRTDKYKRLKAEVEKQSKKLEKKKETITESAGRQQKKK
          MST.F.DTLLIV.F.SV.TALL.EGI.T.VLVYRTDKYKRLKAE.E...K..E........S.....KKK
Retrocopy MSTTFVDTLLIV<FTSVRTALLTEGI>TCVLVYRTDKYKRLKAEAE---KQREEEGNDDRVSWLTTKKKK

Parental  IERQEEKLKNNNRDLSMVRMKSMFAIGFCFTALMGMFNSIFDGRVVAKLPFTPLSYIQGLSHRNLLGDDT
          IERQE.K.K.N.R..S..RMKSMFA.GFCF.ALMG.FNSIF.GRVVAKL...P.S..QG..HR.LLG.DT
Retrocopy IERQEKKRKTNKR--SIARMKSMFAMGFCFPALMGTFNSIFSGRVVAKLS-DPFSFTQGRPHRHLLGGDT

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	38.30 RPM
SRP017611_kidney	0.00 RPM	77.54 RPM
SRP017611_liver	0.00 RPM	39.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1642 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1642 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010009	1 retrocopy	retro_btau_1441,
Canis familiaris	ENSCAFG00000013472	2 retrocopies	retro_cfam_1640, retro_cfam_833,
Echinops telfairi	ENSETEG00000009382	2 retrocopies	retro_etel_1552, retro_etel_570,
Macropus eugenii	ENSMEUG00000011045	2 retrocopies	retro_meug_894, retro_meug_997,
Monodelphis domestica	ENSMODG00000001335	2 retrocopies	retro_mdom_1319, retro_mdom_334,
Oryctolagus cuniculus	ENSOCUG00000008441	2 retrocopies	retro_ocun_1148, retro_ocun_1642 ,
Sarcophilus harrisii	ENSSHAG00000016602	1 retrocopy	retro_shar_790,