RetrogeneDB ID: retro_ptro_546

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:58483249..58484101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAPTM4B
• Ensembl ID: ENSPTRG00000020448
• Aliases: None
• Description: lysosomal protein transmembrane 4 beta [Source:HGNC Symbol;Acc:13646]

Sequence

>retro_ptro_546
TCGGAAGCTCGGAGCTCTCGGGGTATCGAGGAGGCAGGCCCGCGGGCGCACGGGCGAGCGGGCCGGGAGCCGGAGCGGCG
GAGGAGCCGGCAGCAGCGGCGCGGCGGGATCCAGGCGAGGCGGTCGAAGCTCCTGAAAACTTGCGCGCGCGCTCGCGCCA
CTGCGCCCGGAGCGATGAAGATGGTCGCGCCCTGGACGCGGTTCTACTCCAACAGCTGCTGCTTGTGCTGCCATGTCCGC
ACCGGCACCATTCTGCTCGGCGTCTGGTATCTGATCATCAATGCTGTGGTACTGTTGATTTTATTGAGTGCCCTGGCTGA
TCCAGATCAGTATCACTTTTCAAGTTCTGAACTGGGAGGTGACTTTGAGTTCATGGATGATGCCAACATGTGCATTGCCA
TTGCGATTTCTCTTCTCATGATCCTGATATGTGCTATGGCTACTTACGGAGCATACAAGCAACGCGCAGCCTGGATCATC
CCATTCTTCTGTTACCAGATCTTTGACTTTGCCCTGAACATGTTGGTTGCAATCACTGTGCTTATTTATCCAAACTCCAT
TCAGGAATACATACGGCAACTGCCTCCTAATTTTCCCTACAGAGATGATGTCATGTCAGTGAATCCTACCTGTTTGGTCC
TTATTATTCTTCTGTTTATTAGCATTATCTTGACTTTTAAGGGTTACTTGATTAGCTGTGTTTGGAACTGCTACCGATAC
ATCAATGGTAGGAACTCCTCTGATGTCCTGGTTTATGTTACCAGCAATGACACTACGGTGCTGCTACCCCCATATGATGA
TGCCACTGTGAATGGTGCTGCCAAGGAGCCACCGCCACCTTACGTGTCTGCC

Alignment

ORF - retro_ptro_546 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.3 %
• Parental protein coverage: 89.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEARSSRGIEEAGPRAHGRAGREPERRRSRQQRRGGLQARRSKLLKTCARARATAPGAMKMVAPWTRFYS
          .EARSSRGIEEAGPRAHGRAGREPERRRSRQQRRGG.QARRSKLLKTCARARATAPGAMKMVAPWTRFYS
Retrocopy SEARSSRGIEEAGPRAHGRAGREPERRRSRQQRRGGIQARRSKLLKTCARARATAPGAMKMVAPWTRFYS

Parental  NSCCLCCHVRTGTILLGVWYLIINAVVLLILLSALADPDQYHFSSSELGGDFEFMDDANMCIAIAISLLM
          NSCCLCCHVRTGTILLGVWYLIINAVVLLILLSALADPDQYHFSSSELGGDFEFMDDANMCIAIAISLLM
Retrocopy NSCCLCCHVRTGTILLGVWYLIINAVVLLILLSALADPDQYHFSSSELGGDFEFMDDANMCIAIAISLLM

Parental  ILICAMATYGAYKQRAAWIIPFFCYQIFDFALNMLVAITVLIYPNSIQEYIRQLPPNFPYRDDVMSVNPT
          ILICAMATYGAYKQRAAWIIPFFCYQIFDFALNMLVAITVLIYPNSIQEYIRQLPPNFPYRDDVMSVNPT
Retrocopy ILICAMATYGAYKQRAAWIIPFFCYQIFDFALNMLVAITVLIYPNSIQEYIRQLPPNFPYRDDVMSVNPT

Parental  CLVLIILLFISIILTFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDTTVLLPPYDDATVNGAAKEPPPP
          CLVLIILLFISIILTFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDTTVLLPPYDDATVNGAAKEPPPP
Retrocopy CLVLIILLFISIILTFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDTTVLLPPYDDATVNGAAKEPPPP

Parental  YVSA
          YVSA
Retrocopy YVSA

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	0.54 RPM	28.60 RPM
SRP007412_cerebellum	0.00 RPM	14.27 RPM
SRP007412_heart	0.87 RPM	94.14 RPM
SRP007412_kidney	0.13 RPM	40.72 RPM
SRP007412_liver	0.07 RPM	4.58 RPM
SRP007412_testis	1.16 RPM	25.82 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_ptro_546 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DC521300	58483252	58483703	99.3	410	3	406
DC526472	58483252	58483607	98.9	354	1	352

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_546 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,