RetrogeneDB ID: retro_ptro_1569

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:111490571..111491232(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B1
• Ensembl ID: ENSPTRG00000008551
• Aliases: None
• Description: Pan troglodytes platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa) (PAFAH1B1), mRNA. [Source:RefSeq mRNA;Acc:NM_001034091]

Sequence

>retro_ptro_1569
CATGACCATAATGTTTCCTCAGTAGTCATCATGGCCAGTGGAGATCATATAGTGTCCGCCTCAAGGGATGAAACTATAAA
AATGTGGGAAGTGCAAACTGGCTACTGTGTGAAGATGTTCACAGGACAGAGAGAATGGGTACATATGGTACAACCAAATC
AAGATGGCACTCTGATAGCCAGCTGTTCCAATGACCAGACTGTGCGTGTATGGGTCGTAGCAACAATGCAATGCAAGGCT
GAGCTCCGAGAACATGAGCATGTGGTAGAATGCATTTCCTGGGCTCCAGAAAGCTCATATTCTTCCATCTCTGAAGCAAC
AGGCTCTGAGACTAAAAAAAAGTGGTAAATCTGGGCCATTCTTGCTGTCTGGATCCAGGGACAAGACTATTAAGATGTGG
GATGTCAGTACTGGCACGTGCCTCATGACGCTCGTGGGTCATGGTAACTGGGTACGTGAAGTTCTGTTCAGTTCTGGGGG
GAAATTTATTTTGAGTTGTGCTGATGACAAGACCCTACACGTATGGGATTACAAGAACAAGCGATGCATGAAGACCCTCA
ATGCGCATGAACACTTTGTTACCTCCTTGGATTTCCACAAGACGGCACCCTATGTGGTCACTGGCAGCGTAGCTCAAACA
GTAAAAGTGTGGGAGTGCCGT

Alignment

ORF - retro_ptro_1569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.5 %
• Parental protein coverage: 53.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLIASCSNDQTVRV
          HDHNVSSV.IM..GDHIVSASRD.TIKMWEVQTGYCVK.FTG.REWV.MV.PNQDGTLIASCSNDQTVRV
Retrocopy HDHNVSSVVIMASGDHIVSASRDETIKMWEVQTGYCVKMFTGQREWVHMVQPNQDGTLIASCSNDQTVRV

Parental  WVVATKECKAELREHEHVVECISWAPESSYSSISEATGSET-KKSGKPGPFLLSGSRDKTIKMWDVSTGM
          WVVAT..CKAELREHEHVVECISWAPESSYSSISEATGSET....GK.GPFLLSGSRDKTIKMWDVSTG.
Retrocopy WVVATMQCKAELREHEHVVECISWAPESSYSSISEATGSET>XXXGKSGPFLLSGSRDKTIKMWDVSTGT

Parental  CLMTLVGHDNWVRGVLFHSGGKFILSCADDKTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGS
          CLMTLVGH.NWVR.VLF.SGGKFILSCADDKTL.VWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGS
Retrocopy CLMTLVGHGNWVREVLFSSGGKFILSCADDKTLHVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGS

Parental  VDQTVKVWECR
          V.QTVKVWECR
Retrocopy VAQTVKVWECR

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	2.11 RPM	341.10 RPM
SRP007412_cerebellum	3.12 RPM	307.65 RPM
SRP007412_heart	1.69 RPM	120.81 RPM
SRP007412_kidney	1.65 RPM	124.82 RPM
SRP007412_liver	1.08 RPM	55.62 RPM
SRP007412_testis	13.81 RPM	287.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1569 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1569 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1569 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2292
Homo sapiens	retro_hsap_2144
Pongo abelii	retro_pabe_1932

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000007168	2 retrocopies	retro_hsap_2144, retro_hsap_2292,
Monodelphis domestica	ENSMODG00000010776	2 retrocopies	retro_mdom_441, retro_mdom_460,
Mus musculus	ENSMUSG00000020745	1 retrocopy	retro_mmus_2988,
Pongo abelii	ENSPPYG00000007796	1 retrocopy	retro_pabe_1932,
Pan troglodytes	ENSPTRG00000008551	1 retrocopy	retro_ptro_1569 ,
Pan troglodytes	ENSPTRG00000020853	1 retrocopy	retro_ptro_344,
Pan troglodytes	ENSPTRG00000023653	2 retrocopies	retro_ptro_18, retro_ptro_1975,
Sorex araneus	ENSSARG00000002826	4 retrocopies	retro_sara_266, retro_sara_275, retro_sara_364, retro_sara_588,