RetrogeneDB ID: retro_ocun_1843

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019297:41503..42065(+)
• 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_1843
GAATCACTTTAAGGAGACATCAATGACCCTGCCAAGTATGAGATGTTTACATTTCAGAATGGAGGTGTTCAAATTTTATG
CAAATACCCCGAGATTGTCCTGCAATTCAAAATGCAGCTGCTGACAGGGAGACAAGTCCTCTGTGACTTCAGGCAGACAA
AGGAGAGTGGAAACACGGTGTTCATTAAGGCTCTGAAATTCTGTCAATATCAATGATTCAACAACATTTTATTTTTTCCT
ATATAATTTGGACAGTTCTCATGCCAGCTATTACTTCTGCAAACTATCAATTTTTGACCCTCCTCCTTTTCAAGTAGAGA
TTCTCAGAGGAGAATATTTGCATATTTAGGAATCACAAGCTCTGTTGCCAGGTGAAGTTCTGGTTACCCATAGGATGTGC
AGCTTTGCAGTAGTCTACATTTTTGAATGCATATTTATTTTTTGGCTTACAAAGGAGAAATATCAATCAAGCGTGCATGA
CCCAAATAGTGAGTATGTGTTCATAGCAGCAGTGAACACAGCTAAAATATCTGCACTGACAGAACTCTCAGGCACCTGGG
CA

Alignment

ORF - retro_ocun_1843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.72 %
• Parental protein coverage: 84.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVLTGEINDSAKYEMFTFHNGGVQIVCKYPEIVQQFKMQLLKGEQVLCDLRQTKESGNTVSIKALKFCQY
          E.L.G.IND.AKYEMFTF.NGGVQI.CKYPEIV.QFKMQLL.G.QVLCD.RQTKESGNTV.IKALKFCQY
Retrocopy ESL*GDINDPAKYEMFTFQNGGVQILCKYPEIVLQFKMQLLTGRQVLCDFRQTKESGNTVFIKALKFCQY

Parental  QLFNNSVS-FFLYNLDSSHASYYFCKLSTFDPPPFQVEILRGEYLHIYESQ-LCCQLKFWLPIGCAA-FA
          Q.F.N....FFLYNLDSSHASYYFCKLS.FDPPPFQVEILRGEYLHI.ESQ.LCCQ.KFWLPIGCAA.FA
Retrocopy Q*F-NNIL>FFLYNLDSSHASYYFCKLSIFDPPPFQVEILRGEYLHI*ESQ>LCCQVKFWLPIGCAA<FA

Parental  VVYIFGCVFIFWLTKKKYQSSVHDPNSEYMFMAAVNTAKKPTPPELSGTRA
          VVYIF.C.FIFWLTK.KYQSSVHDPNSEY.F.AAVNTAK.....ELSGT.A
Retrocopy VVYIFECIFIFWLTKEKYQSSVHDPNSEYVFIAAVNTAKISALTELSGTWA

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	0.10 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_1843 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1843 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,