RetrogeneDB ID: retro_ocun_1748

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018844:276017..276363(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ICOS
• Ensembl ID: ENSOCUG00000001858
• Aliases: None
• Description: inducible T-cell co-stimulator [Source:HGNC Symbol;Acc:5351]

Sequence

>retro_ocun_1748
TATTCAACAACAGTTTCTTTTGTCGTATATAATTTGGACAGTTCTCATGCCAGATATTACTTGTGCAAACTATCTGTTTT
GATCCTCTTCCTTTTCAAGTAGAGATTCTCAGAGGATAATATTTGCATATTTATGAATTACAGCTCTGTTGCCAGGTGAA
GTTCTGGTTACCCATAGGATGTGCAGCTCTTGCGGTAGTCTACATTTTTGAATGCATATTTATTTTTTGGCTTACAAAAG
AGAAATATCAACCAAGTGTGCATGACCCAAATAGTAACTACATGTTCATAGCAGCAGTGAACACAGCTAAAAATCTACAC
TGACAGAACTCTCTGGCACCTGGGCA

Alignment

ORF - retro_ocun_1748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 52.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FNNSVSFFLYNLDSSHASYYFCKLST-FDPPPFQVEILRGEYLHIYESQLCCQLKFWLPIGCAAFAVVYI
          ....VSF..YNLDSSHA.YY.CKLS..FDP.PFQVEILRG.YLHIYE.QLCCQ.KFWLPIGCAA.AVVYI
Retrocopy YSTTVSFVVYNLDSSHARYYLCKLSV<FDPLPFQVEILRG*YLHIYELQLCCQVKFWLPIGCAALAVVYI

Parental  FGCVFIFWLTKKKYQSSVHDPNSEYMFMAAVNTAK-KPTPPELSGTRA
          F.C.FIFWLTK.KYQ.SVHDPNS.YMF.AAVNTAK.K.T..ELSGT.A
Retrocopy FECIFIFWLTKEKYQPSVHDPNSNYMFIAAVNTAK<KSTLTELSGTWA

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	0.17 RPM
SRP017611_kidney	0.00 RPM	0.20 RPM
SRP017611_liver	0.00 RPM	0.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1748 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1748 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000001858	10 retrocopies	retro_ocun_1052, retro_ocun_1545, retro_ocun_1711, retro_ocun_1742, retro_ocun_1748 , retro_ocun_1822, retro_ocun_1833, retro_ocun_1839, retro_ocun_1843, retro_ocun_1867,