RetrogeneDB ID: retro_ocun_997

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:51845678..51846014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHURC1
• Ensembl ID: ENSOCUG00000001838
• Aliases: None
• Description: churchill domain containing 1 [Source:HGNC Symbol;Acc:20099]

Sequence

>retro_ocun_997
ATGTGTGGGGACTGTGTGGAGAAGGAATATCCCAATCGGGGTAACACTTGTCTGGAGAATGGATCCTTCTTGCTGAACTT
TACAGGTTGTGCAGTGTGCAGTAAGCGGGATTTTATGCTGATCACAAACAAATCCTTGAGAGAGGAAGATGGAGAAGAAA
TAGTTACCTATGATCATCTGTGTAAGAATTGTCATCATGTAATAGCCAAACATGAGTATACCTTCAGTATCATGGATGAA
TTTCAGGAGTACACCATGCTGTGCATGTTATGTGGCAAAGCTGAAGACACAATCAGTATTCTCCCTGACGATCCCCGACA
AATGACCTTGTTATTC

Alignment

ORF - retro_ocun_997 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCGDCVEKEYPNRGNTCLENGSFLLNFTGCAVCSKRDFMLITNKSLREEDGEEIVTYDHLCKNCHHVIAK
          MCGDCVEKEYPNRGNTCLENGSFLLNFTGCAVCSKRDFMLITNKSLREEDGEEIVTYDHLCKNCHHVIAK
Retrocopy MCGDCVEKEYPNRGNTCLENGSFLLNFTGCAVCSKRDFMLITNKSLREEDGEEIVTYDHLCKNCHHVIAK

Parental  HEYTFSIMDEFQEYTMLCMLCGKAEDTISILPDDPRQMTLLF
          HEYTFSIMDEFQEYTMLCMLCGKAEDTISILPDDPRQMTLLF
Retrocopy HEYTFSIMDEFQEYTMLCMLCGKAEDTISILPDDPRQMTLLF

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	0.06 RPM	4.30 RPM
SRP017611_kidney	0.00 RPM	6.59 RPM
SRP017611_liver	0.08 RPM	1.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_997 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_997 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_997 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000004300	1 retrocopy	retro_mluc_2068,
Monodelphis domestica	ENSMODG00000009664	1 retrocopy	retro_mdom_1775,
Mustela putorius furo	ENSMPUG00000006792	1 retrocopy	retro_mputfur_554,
Oryctolagus cuniculus	ENSOCUG00000001838	1 retrocopy	retro_ocun_997 ,
Pteropus vampyrus	ENSPVAG00000011384	1 retrocopy	retro_pvam_406,