RetrogeneDB ID: retro_pabe_2311

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:72742017..72742390(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAPTM4B
• Ensembl ID: ENSPPYG00000018771
• Aliases: None
• Description: lysosomal protein transmembrane 4 beta [Source:HGNC Symbol;Acc:13646]

Sequence

>retro_pabe_2311
GCCATTGCGATTTCTCTTCTCATGATCCTGATATGTGCTATTGGCTACTTACGGAGCATACAAGCAACACACAGCCTAGA
TCCTCCCATTCTTCTGTTACCAGATCTTTAATTTTGCCCTGAATACCTTGGTTGCAATCACTGTCCTTGTTTATCCAAAC
TGCATTCAGGAATACATACGACAACTGCCTCCTAATTTTCCCTACAGAGATGATGTCATGTCAGTGAATCCTACCTGTTT
GGTCCTTATTATTCTTCTGTTTATTAGCATTATCTTGACTTTTAAGGGTTACTTGATTAGCTGTTTTGGAACTGCTATCA
ATGCCAGGAACTCCTCCGATGTCCTGGTTTACGTTACCAGCAATGACACTACC

Alignment

ORF - retro_pabe_2311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.94 %
• Parental protein coverage: 65.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AIAISLLMILICA-MATYGAYKQRAAWIIPFFCYQIFDFALNMLVAITVLIYPNSIQEYIRQLPPNFPYR
          AIAISLLMILICA..ATYGAYKQ..A.I.PFFCYQIF.FALN.LVAITVL.YPN.IQEYIRQLPPNFPYR
Retrocopy AIAISLLMILICA>LATYGAYKQHTA*ILPFFCYQIFNFALNTLVAITVLVYPNCIQEYIRQLPPNFPYR

Parental  DDVMSVNPTCLVLIILLFISIILTFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDTT
          DDVMSVNPTCLVLIILLFISIILTFKGYLISC.......IN.RNSSDVLVYVTSNDTT
Retrocopy DDVMSVNPTCLVLIILLFISIILTFKGYLISCFGTA---INARNSSDVLVYVTSNDTT

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	36.71 RPM
SRP007412_cerebellum	0.00 RPM	18.97 RPM
SRP007412_heart	0.03 RPM	49.79 RPM
SRP007412_kidney	0.07 RPM	63.38 RPM
SRP007412_liver	0.00 RPM	48.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2311 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 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,
Macaca mulatta	ENSMMUG00000008926	1 retrocopy	retro_mmul_532,
Nomascus leucogenys	ENSNLEG00000003756	1 retrocopy	retro_nleu_1531,
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,