RetrogeneDB ID: retro_ocun_813

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:94059130..94059462(+)
• Located in intron of: ENSOCUG00000013272

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC6B
• Ensembl ID: ENSOCUG00000002171
• Aliases: None
• Description: trafficking protein particle complex 6B [Source:HGNC Symbol;Acc:23066]

Sequence

>retro_ocun_813
GAAGGGTTTACAAAAGATACTGCGAGGTTCATGGATGAATAAGACATCACGAAGTTAATTTGTAAAAGTTTCTGGACTAC
AGTATTCAAGAAACAAATTGACACTTTAAGGAAAAATCATTCAGGGCATCTATGTGCTTCAGGACAACAGATTTCATTTG
CTTACTCAGATACCTGAGGGAAAACAGTGTTTGGAATACACGTCTAAGTATTTAGCATTTACAGGTGGCTTAATCAGAGG
TGGCTTGTCAAACTTGTCGATAAAAAGGACTGTAAACAGCTGCACTGTCATCAATGCCTGCCTGCAAATTTCCAGTGATG
ATACAGAAGCTG

Alignment

ORF - retro_ocun_813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.68 %
• Parental protein coverage: 69.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERFTKDTARFKDELDIMKFICKDFWTTVFKKQIDNLRTNH-QGIYVLQDNKFRLLTQMSAGKQYLEHASK
          E.FTKDTARF.DE.DI.K.ICK.FWTTVFKKQID.LR.NH.QGIYVLQDN.F.LLTQ...GKQ.LE..SK
Retrocopy EGFTKDTARFMDE*DITKLICKSFWTTVFKKQIDTLRKNH>QGIYVLQDNRFHLLTQIPEGKQCLEYTSK

Parental  YLAFTCGLIRGGLSNLGIKSIV-TAEVSSMPACKFQVMIQKL
          YLAFT.GLIRGGLSNL.IK..V.TA..SSMPACKF.VMIQKL
Retrocopy YLAFTGGLIRGGLSNLSIKRTV>TAALSSMPACKFPVMIQKL

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	16.17 RPM
SRP017611_kidney	0.10 RPM	11.96 RPM
SRP017611_liver	0.00 RPM	6.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_813 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_813 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013828	1 retrocopy	retro_etel_1104,
Myotis lucifugus	ENSMLUG00000002627	2 retrocopies	retro_mluc_1179, retro_mluc_663,
Mus musculus	ENSMUSG00000020993	2 retrocopies	retro_mmus_1734, retro_mmus_2069,
Oryctolagus cuniculus	ENSOCUG00000002171	1 retrocopy	retro_ocun_813 ,
Sarcophilus harrisii	ENSSHAG00000001400	1 retrocopy	retro_shar_235,
Ictidomys tridecemlineatus	ENSSTOG00000002897	2 retrocopies	retro_itri_476, retro_itri_795,
Tupaia belangeri	ENSTBEG00000003331	1 retrocopy	retro_tbel_4529,