RetrogeneDB ID: retro_ocun_1750

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018844:694220..694718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM160
• Ensembl ID: ENSOCUG00000023097
• Aliases: None
• Description: transmembrane protein 160 [Source:HGNC Symbol;Acc:26042]

Sequence

>retro_ocun_1750
TTGCTGCCTCAGCGGCCCTGGAGCGGGGTTGCCCGGGGGTCCTTCGCCCCTGGCCACGGCCCCCGCGCCGGGGCTTCGCC
GCCTCCAGTGTCTGAGCTGGACCGCGCGGACGCCTGGCTCCTCCGAAAGGCGCGTGAGACAGCCTTCCTTTCCTGGTTCC
TCAATGGCCTCCTGGCATCGGGCTTCGGGGTCATCTCCTTCGTGCAGAACTACATGGGCCGGGAAGCCGCCTATGGCTTC
TTCCTGCTGGGCGGCCTGTGCGTGGTGTGGGGCGGCGCCTCCTACGCCGTGGGCCTGGCCTTGCTGCGAGGCCCCGTGCA
GCTGTCGCTAGGCGGCGCGGCTGCGGGCATGGGCGCCGTGCTGGCCGCCAGCCTGCTGTGGGCCTGCGCTGTCGGCCTCT
ACATGGGTCAGCTGGAGCTGGACGTGGAGCTGGTGCCGGAGAACGACGGGACGGCCGCCGCAGAGGGCCCGGACGAGGCA
GGACGGCCGCCGCCAGAG

Alignment

ORF - retro_ocun_1750 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.17 %
• Parental protein coverage: 88.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPPQRPRSGGARGSFAPGHGPRAGASPPPVSELDRADAWLLRKAHETAFLSWFRNGLLASGIGVISFMQS
          L.PQRP.SG.ARGSFAPGHGPRAGASPPPVSELDRADAWLLRKA.ETAFLSWF.NGLLASG.GVISF.Q.
Retrocopy LLPQRPWSGVARGSFAPGHGPRAGASPPPVSELDRADAWLLRKARETAFLSWFLNGLLASGFGVISFVQN

Parental  DMGREAAYGFFLLGGLCVVWGGASYAVGLAALRGPMQLSVGGAAAGMGAVLAASLLWACAVGLYMGQLEL
          .MGREAAYGFFLLGGLCVVWGGASYAVGLA.LRGP.QLS.GGAAAGMGAVLAASLLWACAVGLYMGQLEL
Retrocopy YMGREAAYGFFLLGGLCVVWGGASYAVGLALLRGPVQLSLGGAAAGMGAVLAASLLWACAVGLYMGQLEL

Parental  DVELVPEDDGTAAAEGPDEAGRPPPE
          DVELVPE.DGTAAAEGPDEAGRPPPE
Retrocopy DVELVPENDGTAAAEGPDEAGRPPPE

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	0.17 RPM	8.22 RPM
SRP017611_kidney	0.10 RPM	11.55 RPM
SRP017611_liver	0.46 RPM	3.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1750 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1750 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1750 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000017997	1 retrocopy	retro_etel_2100,
Homo sapiens	ENSG00000130748	1 retrocopy	retro_hsap_1828,
Gorilla gorilla	ENSGGOG00000013410	1 retrocopy	retro_ggor_2165,
Oryctolagus cuniculus	ENSOCUG00000023097	1 retrocopy	retro_ocun_1750 ,
Pongo abelii	ENSPPYG00000010166	1 retrocopy	retro_pabe_1498,
Pan troglodytes	ENSPTRG00000011200	1 retrocopy	retro_ptro_1165,
Rattus norvegicus	ENSRNOG00000015304	1 retrocopy	retro_rnor_1176,