RetrogeneDB ID: retro_ocun_336

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:10034272..10034698(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2orf47
• Ensembl ID: ENSOCUG00000017946
• Aliases: None
• Description: chromosome 2 open reading frame 47 [Source:HGNC Symbol;Acc:26198]

Sequence

>retro_ocun_336
GAGGCTTTTGCTTATGTATCCAAGTTGCTGTCACAGAGTAAATTTGATCTTTTGGAAGAAATTGTGGCCAAAGAGGTGCT
ACATGTATTGAAAGAAAAGGTTACTTCTCTACCTGATAACCATAAAAGTGCCCTTGCTGCTGACATAGATGAAATTGTAT
ATACATCAACAGGAGACATCTCCATTTACTATGATGAGAAAGGAAGGAAGTTTGTTAACATCCTGATGTGCTTTTGGTAT
CTAACCAGTGCCAACGTCCCCAATGAAACTATACGTGGAGCCAGTGTATTCCAAGTTAAGTTGGGGGATCAGAATGTGGA
AACTAAACAACTTCTTAGTGCAAACTATGAATTTCAGAGAGAATTTACACAAGGAGTAAAGCCCAACTGGACCATTGCAC
GGATTGAAAACCCAAAATTATTGGAA

Alignment

ORF - retro_ocun_336 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.48 %
• Parental protein coverage: 50.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAFAYVSKLLSQCKFDLLEELVAKEVLHVLKEKVTSLPDNHKSALAADIDEIVYTSTGDISIYYDEKGRK
          .AFAYVSKLLSQ.KFDLLEE.VAKEVLHVLKEKVTSLPDNHKSALAADIDEIVYTSTGDISIYYDEKGRK
Retrocopy EAFAYVSKLLSQSKFDLLEEIVAKEVLHVLKEKVTSLPDNHKSALAADIDEIVYTSTGDISIYYDEKGRK

Parental  FVNILMCFWYLTSANVPNETIRGASVFQVKLGDQNVETKQLLSASYEFQREFTQGVKPNWTIARIEHPKL
          FVNILMCFWYLTSANVPNETIRGASVFQVKLGDQNVETKQLLSA.YEFQREFTQGVKPNWTIARIE.PKL
Retrocopy FVNILMCFWYLTSANVPNETIRGASVFQVKLGDQNVETKQLLSANYEFQREFTQGVKPNWTIARIENPKL

Parental  LE
          LE
Retrocopy LE

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	0.11 RPM	4.30 RPM
SRP017611_kidney	0.00 RPM	9.73 RPM
SRP017611_liver	0.00 RPM	3.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_336 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_336 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000017946	1 retrocopy	retro_ocun_336 ,