RetrogeneDB ID: retro_pabe_1932

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:19367185..19368136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B1
• Ensembl ID: ENSPPYG00000007796
• Aliases: PAFAH1B1, LIS1, PAFAHA
• Description: platelet-activating factor acetylhydrolase IB subunit alpha [Source:RefSeq peptide;Acc:NP_001124853]

Sequence

>retro_pabe_1932
CCAGAAAAATACACATTGAGTGGTCACAGGAGTCCAATCACTCGAGTCATTTTCCATCCTGTGTTCAGTGTTATGGTCTC
TGCTTCAGAGGATGCTACAGTTAAGGTGTGGGATTATGAGACTGGAGATTTTGAAAGAACTCTTAAAGGAAGGACATACA
GACTCTGTACAGGACATTTCATTTGACCACAGTGGCAAGTTTCTGGCTTCCTGTTCTGCAGCTATGACCATTAAACTATG
GGATTTTCAGGACTTTGAATGCATCAGAACCATGCACGGTCATGGTTCCCCATGACCATAATGTTTCCTCAGTAGCCATC
ATGCCCAGTGGAGATCATATAGTGTCTGCCTCAAGGGATAAAACTATAAAAATGTGGGAAGTGCAAACTGGCTACTGTGT
GAAGACGCTCACAGGACACAGAGAATGGGTATGTACAGTACAACCAAATCAAGATGGCACTCTGATAGCCAGCTGTTCCA
ATGACCAGACTGTGCGTGTATGGGTCGTAGCAACAATGCAATGCAAGGCTGAGCTCTAAGAACATGAGCATGTGGTAGAA
TGCATTTCCTGGGCTCCAGAAAGCTCATATTCTTCCATCTCTGAAGCAACAGGCTCTGAGACTAAAAAAAAGTGGTAAAC
CTGGGCCATTCTTGCTGTCTGGATCCAGGGACAAGACTATTAAGATGTGGCATGTCAGTACTGGCATGTGCCTTATGACC
CTCGTGGGTCATGGTAACTGGGTACCTGGAGTTCTGTTCAATTCTGGGGGGATATTTATTTTGAGTTGTGCTGATGACAA
GACCCTACACGTATGGGATTACAAGAACAAGCGATGATGCATGAAGACCCTCAATGCGCATGAACACTTTGTTACCTCCT
TGGATTTCCACAAGACGGCACCCTATGTGGTCACTGGCAGCATAGATCAAACAGTAAAAGTGTGGGAGTGC

Alignment

ORF - retro_pabe_1932 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.46 %
• Parental protein coverage: 75.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PEKYALSGHRSPVTRVIFHPVFSVMVSASEDATIKVWDYETGDFERT-LK-GHTDSVQDISFDHSGKLLA
          PEKY.LSGHRSP.TRVIFHPVFSVMVSASEDAT.KVWDYETGDFERT.LK.GHTDSVQDISFDHSGK.LA
Retrocopy PEKYTLSGHRSPITRVIFHPVFSVMVSASEDATVKVWDYETGDFERT>LKEGHTDSVQDISFDHSGKFLA

Parental  SCSADMTIKLW---DFQ-GFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTG
          SCSA.MTIKLW...DF....E....M..HDHNVSSVAIMP.GDHIVSASRDKTIKMWEVQTGYCVKT.TG
Retrocopy SCSAAMTIKLWDFQDFE>ASEPCTVMVPHDHNVSSVAIMPSGDHIVSASRDKTIKMWEVQTGYCVKTLTG

Parental  HREWVRMVRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGSET-
          HREWV..V.PNQDGTLIASCSNDQTVRVWVVAT..CKAEL.EHEHVVECISWAPESSYSSISEATGSET.
Retrocopy HREWVCTVQPNQDGTLIASCSNDQTVRVWVVATMQCKAEL*EHEHVVECISWAPESSYSSISEATGSET>

Parental  KKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADDKTLRVWDYKNKR
          ...GKPGPFLLSGSRDKTIKMW.VSTGMCLMTLVGH.NWV.GVLF.SGG.FILSCADDKTL.VWDYKNKR
Retrocopy XXXGKPGPFLLSGSRDKTIKMWHVSTGMCLMTLVGHGNWVPGVLFNSGGIFILSCADDKTLHVWDYKNKR

Parental  -CMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWEC
          .CMKTLNAHEHFVTSLDFHKTAPYVVTGS.DQTVKVWEC
Retrocopy *CMKTLNAHEHFVTSLDFHKTAPYVVTGSIDQTVKVWEC

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	0.06 RPM	318.97 RPM
SRP007412_cerebellum	0.12 RPM	301.21 RPM
SRP007412_heart	0.03 RPM	86.91 RPM
SRP007412_kidney	0.00 RPM	94.70 RPM
SRP007412_liver	0.03 RPM	53.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1932 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1932 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1932 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2292
Homo sapiens	retro_hsap_2144
Pan troglodytes	retro_ptro_1569

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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 ,
Pongo abelii	ENSPPYG00000014001	2 retrocopies	retro_pabe_320, retro_pabe_321,
Pongo abelii	ENSPPYG00000019140	1 retrocopy	retro_pabe_274,
Pan troglodytes	ENSPTRG00000008551	1 retrocopy	retro_ptro_1569,
Sorex araneus	ENSSARG00000002826	4 retrocopies	retro_sara_266, retro_sara_275, retro_sara_364, retro_sara_588,