RetrogeneDB ID: retro_btau_786

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:12622719..12623397(-)
• Located in intron of: ENSBTAG00000009427

Retrocopy information

• Ensembl ID: ENSBTAG00000046974
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LAPTM4B
• Ensembl ID: ENSBTAG00000016959
• Aliases: None
• Description: lysosomal-associated transmembrane protein 4B [Source:RefSeq peptide;Acc:NP_991371]

Sequence

>retro_btau_786
ATGAAGATGGTGGCCCCCTGGACACGGTTCTCCTCCAACAGCTGCTGCCTCTGCTGCCATGTCCGCACTGGCACCATCCT
GCTCGGCGTCTGGTACTTGATCCTCAATGCCGTGGTACTGCTGATTCTGTTGAGCGCCCTGGATGATCCAGATCATTACC
ACTTTTCAAGTTCTGAACTCGGGGGTGACTTTGAGTTCATGGATGATGCCAACATGTGCATTGCCATCGCGATTTCTGTT
CTCATGATCCTTATCTGTGCCATGGCTACGTACGGCGCATACAAGCAACGCGCAGGCTGGATCATCCCATTCTTCTGCTA
CCAGATCTTTGATTTTGCCCTCAACACCTTGGTTGCGGTCACCGTACTTGTTTATCCAAACTCCATCCAGGAATATATAT
GACAGCTGCCTCCTGATTTTCCTTACAAAGATGATATCATGTCAGTGAATCCTACCTGTTTGGTCCTCATTATTCTTCTG
TTCATCAGCATTATCTTGGCTTTTAAGGGTTACTTGATTAGCTGTGTTTGGAACTGCTACCGATATATCAATGGCAGGAA
CTCCTCTGATGTCCTGGTTTATGTTACCAGCAACGACACTACAGTGCTGCTACCCCCGTACGATGACGCCACTGTGAACA
GCGCCACCAAGGAGCCGCCGCCCCCGTACGTGTCTGCC

Alignment

ORF - retro_btau_786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKMVAPWTRFYSNSCCLCCHVRTGTILLGVWYLILNAVVLLILLSALADPDHYHFSSSELGGDFEFMDDA
          MKMVAPWTRF.SNSCCLCCHVRTGTILLGVWYLILNAVVLLILLSAL.DPDHYHFSSSELGGDFEFMDDA
Retrocopy MKMVAPWTRFSSNSCCLCCHVRTGTILLGVWYLILNAVVLLILLSALDDPDHYHFSSSELGGDFEFMDDA

Parental  NMCIAIAISVLMILICAMATYGAYKQRAAWIIPFFCYQIFDFALNTLVAVTVLVYPNSIQEYIRQLPPDF
          NMCIAIAISVLMILICAMATYGAYKQRA.WIIPFFCYQIFDFALNTLVAVTVLVYPNSIQEYI.QLPPDF
Retrocopy NMCIAIAISVLMILICAMATYGAYKQRAGWIIPFFCYQIFDFALNTLVAVTVLVYPNSIQEYI*QLPPDF

Parental  PYKDDIMSVNPTCLVLIILLFISIILAFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDTTVLLPPYDDA
          PYKDDIMSVNPTCLVLIILLFISIILAFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDTTVLLPPYDDA
Retrocopy PYKDDIMSVNPTCLVLIILLFISIILAFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDTTVLLPPYDDA

Parental  TVNSATKEPPPPYVSA
          TVNSATKEPPPPYVSA
Retrocopy TVNSATKEPPPPYVSA

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
ERP005899_liver	3.82 RPM	148.23 RPM
ERP005899_muscle	0.95 RPM	342.92 RPM
SRP017611_brain	0.59 RPM	33.16 RPM
SRP017611_kidney	2.37 RPM	114.87 RPM
SRP017611_liver	4.76 RPM	212.03 RPM
SRP030211_testis	0.60 RPM	118.98 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_786 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_786 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_786 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786 ,
Bos taurus	ENSBTAG00000020894	1 retrocopy	retro_btau_575,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027,
Myotis lucifugus	ENSMLUG00000003618	1 retrocopy	retro_mluc_1182,
Macaca mulatta	ENSMMUG00000008926	1 retrocopy	retro_mmul_532,
Mus musculus	ENSMUSG00000022257	1 retrocopy	retro_mmus_1549,
Nomascus leucogenys	ENSNLEG00000003756	1 retrocopy	retro_nleu_1531,
Oryctolagus cuniculus	ENSOCUG00000013689	1 retrocopy	retro_ocun_627,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856, retro_ogar_2902,
Pongo abelii	ENSPPYG00000018771	2 retrocopies	retro_pabe_2311, retro_pabe_279,
Pan troglodytes	ENSPTRG00000020448	1 retrocopy	retro_ptro_546,
Tursiops truncatus	ENSTTRG00000003124	1 retrocopy	retro_ttru_76,