RetrogeneDB ID: retro_ptro_41

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:17985232..17985856(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039747
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GLTP
• Ensembl ID: ENSPTRG00000005431
• Aliases: None
• Description: glycolipid transfer protein [Source:HGNC Symbol;Acc:24867]

Sequence

>retro_ptro_41
ATGGCTCTGCTGGCCGAACACCTGCTGAAGCCGTTGCCCGCGGACAAGCAGATCGAGACTGGGCCCTTCCTCGAGGCGGT
GTCCCACCTGCCGCCCTTCTTCGATTGCCTTGGGTCCCCAGTGTTTACTCCCATCAAGGCAGACATAAGCAGCAACATCA
CAAAAATCAAAGCTGTGTACGACACCAACCCAGCCAAGTTCCGGACCCTGCAGAACATCCTGGAGGTGGAGAAAGAAATG
TATGGAGCAGAGCGGCCCAAAGTAGGGGCCACGCTGGCGCTGATGTGGCTGAAAAGAGGCCTCCGCTTCATCCAGGTCTT
CCTCCAGAGCATCTGCAACGAGGAGCGGGACGAGAACCACCCCAACCTCATTCGCGTCAACGCCACCAAGGCCTACGAAA
TGGCCCTCATGAAGTACCACGGCTGGATCGTGCAGATCTTCCAGGCAGCACTGCACGCAGCCTCCTGTAAGTCCGACTTG
CTGAAAGCGCTCTCCAAGGGGCAGAATGTGACGGAGGAGGAGTGCCTGGAGAAGATCCGCCTCTTCCTAGTCAACTACAT
GGCGACCATCGATGTCATCTACGAGAGGTACACCCAGATGAACGCTGAGCTAAACTACAAGGTG

Alignment

ORF - retro_ptro_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DCLGSPVFTPIKADISGNITKIKAVYDTNPAKFRTLQNILEVEKEMYGAEWPKVGATLALMWLKRGLRFI
          DCLGSPVFTPIKADIS.NITKIKAVYDTNPAKFRTLQNILEVEKEMYGAE.PKVGATLALMWLKRGLRFI
Retrocopy DCLGSPVFTPIKADISSNITKIKAVYDTNPAKFRTLQNILEVEKEMYGAERPKVGATLALMWLKRGLRFI

Parental  QVFLQSICDGERDENHPNLIRVNATKAYEMALKKYHGWIVQKIFQAALYAAPYKSDFLKALSKGQNVTEE
          QVFLQSIC..ERDENHPNLIRVNATKAYEMAL.KYHGWIVQ.IFQAAL.AA..KSD.LKALSKGQNVTEE
Retrocopy QVFLQSICNEERDENHPNLIRVNATKAYEMALMKYHGWIVQ-IFQAALHAASCKSDLLKALSKGQNVTEE

Parental  ECLEKIRLFLVNYTATIDVIYEMYTQMNAELNYKV
          ECLEKIRLFLVNY.ATIDVIYE.YTQMNAELNYKV
Retrocopy ECLEKIRLFLVNYMATIDVIYERYTQMNAELNYKV

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	1.39 RPM	13.26 RPM
SRP007412_cerebellum	0.32 RPM	7.21 RPM
SRP007412_heart	0.35 RPM	5.07 RPM
SRP007412_kidney	1.78 RPM	17.65 RPM
SRP007412_liver	0.75 RPM	6.32 RPM
SRP007412_testis	0.32 RPM	13.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_41 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_41 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_41 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_755
Pongo abelii	retro_pabe_28

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034092	1 retrocopy	retro_cjac_1284,
Echinops telfairi	ENSETEG00000016033	1 retrocopy	retro_etel_1197,
Homo sapiens	ENSG00000139433	1 retrocopy	retro_hsap_755,
Myotis lucifugus	ENSMLUG00000012545	5 retrocopies	retro_mluc_1056, retro_mluc_1902, retro_mluc_2135, retro_mluc_2397, retro_mluc_658,
Macaca mulatta	ENSMMUG00000022761	1 retrocopy	retro_mmul_2261,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28,
Pan troglodytes	ENSPTRG00000005431	1 retrocopy	retro_ptro_41 ,
Pan troglodytes	ENSPTRG00000019036	1 retrocopy	retro_ptro_688,
Rattus norvegicus	ENSRNOG00000001192	1 retrocopy	retro_rnor_2465,
Ictidomys tridecemlineatus	ENSSTOG00000004484	1 retrocopy	retro_itri_973,