RetrogeneDB ID: retro_ocun_1084

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:22803350..22804115(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023563
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC9C2
• Ensembl ID: ENSOCUG00000015222
• Aliases: None
• Description: solute carrier family 9, member C2 (putative) [Source:HGNC Symbol;Acc:28664]

Sequence

>retro_ocun_1084
GCGGAGCCTCGGGCCGGCGAGGTAATTGTGGAATTAATGGAGCCAGAAGGACCCTCAGAATCAGTGAGTTCAGAAAAATC
AGTATTTTTTTCATCTCATGAAGACGATAATCAAGAATCAGAATCAGAATCCACAAGCACCGTGAACCCTCTCCTACAGC
CTGCTCTCACAGGGGATGTCGAAGGTTTGCAGGAGATCTTTGAGGATCCTGAGAATCCTCATCATGAACACGCCATGCAG
CTAGTCTTGCAAGAAGACATTGTCGGGAGAAATTTGTTGTATGCAGCTTGCATGGCTGGGCAAAGTGGCATTATTAGAGC
CTTGGCAAAATATGGCGTGAATCTGAACGAGAAAACTGCCAGAGGGTACACACTCTTGCACTGTGCTGCAGCCTGGGGCT
GTTTGGAAACTTTGAAAGCCCTGGTGGAACTGGACGTCGATATAGAAGCTTTGAACTTCCGTGAAGAAAAAGCTCGAGAT
GTTGCAGCTCGGTATTCCCAGACGGAGTGTGTTGAATTCCTGGACTGGGCAGATGCAAGGCTGGCTCTGAAAAAATATAT
CGCAAAGGCCACTTTGGCTGTTACTGACACTGAAAAGGGACCAGGGAAGCTCTTTATGGAAGATAAGAATACCATCCTCA
ATGCATGCCGTGCAAAAAATGAATGGTTGGAAACCCACGCGGATGCTTCTGTTAATGAGCTCTTTGAGCAGAGACAACAA
TTAGAAGATATTGTGACTCCTATCCTCACAAAAATGGCTACACCC

Alignment

ORF - retro_ocun_1084 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.69 %
• Parental protein coverage: 98.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANNNAWKVIVELMEPEGPSESVSSEKSVFFSSHEDDNQESESESAGTANPLLQPALTGDVEGLQEIFEDP
          A...A..VIVELMEPEGPSESVSSEKSVFFSSHEDDNQESESES..T.NPLLQPALTGDVEGLQEIFEDP
Retrocopy AEPRAGEVIVELMEPEGPSESVSSEKSVFFSSHEDDNQESESESTSTVNPLLQPALTGDVEGLQEIFEDP

Parental  ENPHHEHAMQLVLQEDIVGRNLLYAACMAGQSGIIRALAKYGVNLNEKTARGYTLLHCAAAWGRLETLKA
          ENPHHEHAMQLVLQEDIVGRNLLYAACMAGQSGIIRALAKYGVNLNEKTARGYTLLHCAAAWG.LETLKA
Retrocopy ENPHHEHAMQLVLQEDIVGRNLLYAACMAGQSGIIRALAKYGVNLNEKTARGYTLLHCAAAWGCLETLKA

Parental  LVELDVDIEALNFREEKARDVAARYSQTECVEFLDWADARLALKKYIAKATLAVTDTEKGPGKLFKEDKN
          LVELDVDIEALNFREEKARDVAARYSQTECVEFLDWADARLALKKYIAKATLAVTDTEKGPGKLF.EDKN
Retrocopy LVELDVDIEALNFREEKARDVAARYSQTECVEFLDWADARLALKKYIAKATLAVTDTEKGPGKLFMEDKN

Parental  TILNACRAKNEWLETHADASINELFEQRQQLEDIVTPILTKMATP
          TILNACRAKNEWLETHADAS.NELFEQRQQLEDIVTPILTKMATP
Retrocopy TILNACRAKNEWLETHADASVNELFEQRQQLEDIVTPILTKMATP

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	1.60 RPM	7.01 RPM
SRP017611_kidney	3.95 RPM	10.85 RPM
SRP017611_liver	1.46 RPM	8.17 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1084 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1084 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1084 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000015222	1 retrocopy	retro_ocun_1084 ,