RetrogeneDB ID: retro_ocun_627

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:125499856..125500207(+)
• Located in intron of: ENSOCUG00000004703

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAPTM4B
• Ensembl ID: ENSOCUG00000013689
• Aliases: None
• Description: lysosomal protein transmembrane 4 beta [Source:HGNC Symbol;Acc:13646]

Sequence

>retro_ocun_627
TGTTACTGGATCTTTGATTTTTTTCTGAACACCTTGGTTACAGTCACTGTGCTTGTTTATCTATTCAGGAATACATAAGT
TAACTGCCTCCTAATTTCCCTGGCAAGGATGACATCATGTCAGTGAATCCTACCTGTTTGATTGTGACTATTCTGCTTAT
CAGCAATATCTTGACTGAAGCATTACTTGATTAGCTGCGTTTGAAACTGTTACCAAAACATCAGTAGCGGGAATGCCTCT
GATGTCCTGGTTTATATCACCAGCAATAACACTGAAATGTTGTTACCTCCACTTTATGGTACCACTGTTAATGGCTCTGC
TAAGGAGCCACCACTGCCTTCTGTGTCTGCC

Alignment

ORF - retro_ocun_627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.23 %
• Parental protein coverage: 54.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CYQIFDFALNTLVAVTVLVYPN-SIQEYIRQLPPNFPYREDIMAVNPTCLVLII-LLFISIILTFKGYLI
          CY.IFDF.LNTL..VTV.V....SIQEYI..LPPNFP...DIM.VNPTC..LI..L...S.I...K.YLI
Retrocopy CYWIFDFFLNTL--VTVTVLVY<SIQEYIS*LPPNFPGKDDIMSVNPTC--LIV>LFCLSAIS*LKHYLI

Parental  SCVWNCYRYINSRNASDVLVYVTSNDTTVLLPPYDDAAVNGAAKEPPPPYVSA
          SCV.NCY..I.S.NASDVLVY.TSN.T..LLPP.....VNG.AKEPP.P.VSA
Retrocopy SCV*NCYQNISSGNASDVLVYITSNNTEMLLPPLYGTTVNGSAKEPPLPSVSA

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	57.89 RPM
SRP017611_kidney	0.00 RPM	68.82 RPM
SRP017611_liver	0.00 RPM	43.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_627 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_627 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027,
Myotis lucifugus	ENSMLUG00000003618	1 retrocopy	retro_mluc_1182,
Mus musculus	ENSMUSG00000022257	1 retrocopy	retro_mmus_1549,
Oryctolagus cuniculus	ENSOCUG00000013689	1 retrocopy	retro_ocun_627 ,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856, retro_ogar_2902,