RetrogeneDB ID: retro_ocun_1151

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 21:15238557..15239178(+)
• Located in intron of: ENSOCUG00000014685

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALM
• Ensembl ID: ENSOCUG00000006325
• Aliases: None
• Description: galactose mutarotase (aldose 1-epimerase) [Source:HGNC Symbol;Acc:24063]

Sequence

>retro_ocun_1151
GCAACGGCCCGTGGGTTTGGATGTCTGGATGGAGGACTCCAAGGGTTTGATTAGGTTCTCCAGATACCTCAGATACTGCC
AAATGGTGTCCGGTTCTCTAGTGTCGGTGCAGATGCTGAGGAAGGCTACACCACAGAGTTAAAAATTTTGCATGGCATAC
ACCTCGGGTGGCAGGGAACTCGTGGTCAACTACAGAGCACAGGCCAGTCCAACCACATTGGTCAGTCCCACCAACCATTC
TTCTATCAGCTTGTCAGGGCAGGGTTCCCCCAATATATAGGACCATGAAGTTACCACAGAAACTGATGCTTGTTTGCCAG
TGAGTGAAACCTTTATTGCTACAGGAGAAGTTGCTCCAGTGCCAGAAACTACATTCCAACTGAGAAAGCCAGTAGAGCTT
GGAAAACACCTGTAGCAGTCCCCATCGATGGCTTTGACTATCACTTGTCTGAAGGGATCTAAAGAAAAACATTTGTGTGC
AAGGGTGCATCCTTACGGAGGTGGGCAGGTACTAAAAGTGTACACCAACCAGCCTAGGGTGGAGTTTTACATGCCAGCTT
CCCGGATGGCACACTGAGGAACAAGGCCAGAGGGGTCTATCGCAAGCCCTCTGGGGAGTGC

Alignment

ORF - retro_ocun_1151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.85 %
• Parental protein coverage: 60.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AINNGPNSLHGGLRGFDKVLWTPQVLPNGVQFSRVSADGEEGYPGELKVW-VTYTLDGGELVVNYRAQAS
          A...G...L.GGL.GFD.VL..PQ.LPNGV.FS.V.AD.EEGY..ELK.....YT..G.ELVVNYRAQAS
Retrocopy ATARGFGCLDGGLQGFD*VLQIPQILPNGVRFSSVGADAEEGYTTELKIL>MAYTSGGRELVVNYRAQAS

Parental  QTTPVNLTNHSYFNLAGQGSPNIYDHEVTIDADAFLPVNETLIPTGEVAPVQGTAFDLRKPVELGKHLQQ
          .TT.V..TNHS...L.GQGSPNI.DHEVT...DA.LPV.ET.I.TGEVAPV..T.F.LRKPVELGKHL.Q
Retrocopy PTTLVSPTNHSSISLSGQGSPNI*DHEVTTETDACLPVSETFIATGEVAPVPETTFQLRKPVELGKHL*Q

Parental  -FHINGFDHNFCLKGSKEKHF-CARVQHAGSGRVLEVYTTQPGVQFYT-ANFLDGTLKGKGGAVYPKHSG
          ...I.GFD......G...K.F.CARV...G.G.VL.VYT.QP.V.FY..A.F.DGTL..K...VY.K.SG
Retrocopy <VPIDGFDYHLS-EGI*RKTF>CARVHPYGGGQVLKVYTNQPRVEFYM<ASFPDGTLRNKARGVYRKPSG

Parental  FC
          .C
Retrocopy EC

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	9.82 RPM
SRP017611_kidney	0.10 RPM	238.49 RPM
SRP017611_liver	0.15 RPM	191.61 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1151 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1151 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015006	1 retrocopy	retro_meug_2094,
Macaca mulatta	ENSMMUG00000008248	1 retrocopy	retro_mmul_761,
Oryctolagus cuniculus	ENSOCUG00000006325	1 retrocopy	retro_ocun_1151 ,
Sus scrofa	ENSSSCG00000008486	1 retrocopy	retro_sscr_147,
Tupaia belangeri	ENSTBEG00000003695	2 retrocopies	retro_tbel_2040, retro_tbel_2771,