RetrogeneDB ID: retro_pabe_2709

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:180732785..180733427(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOA1BP
• Ensembl ID: ENSPPYG00000000713
• Aliases: None
• Description: apolipoprotein A-I binding protein [Source:HGNC Symbol;Acc:18453]

Sequence

>retro_pabe_2709
CAGGAGGAAGCCCAGGCCGTGGACCAGGAGCTATTTAACGAGTACCAGTTCAGCGTGGACCGATTTATGGAGCTGGCCGG
GCTGAGCTGTGCCACAGCCATCGCCAAGGCGTGTACCCCCACGTCCATGTCCAGGAGCCCCCCAACCGTCCTGGTCATCT
GTGGCCCGGGGCATAATGGAGGAGATGGTCTGGTCTGTGCTCCACACCTCAAACTCTTTGGCTAACCAGCCAACCATCTA
TTACCCCAAAAGGCCTAACAAGCCCCTCTTCATTGCGTTAGTGACCCAGGGTCAGAAAACGGACATCCCTTTCCTTGGGG
AAATGCGCTCAGAGCCCGTGATGATTGAGCTGTATGAGCTGGTGGTGGATGCCATCTTCGGCTTCAGCTTCGAGGGTGAT
GTTCGGGAACGTTCCACAGCATCCTGAGTGTCCTGAAGGGACTCACTGTGCCCATTGCCGGCATCAACATTCCCTCAGGA
TGGGATGTGGAGAAGGGAAACTCTGGAGGGATCCAGCCAGACTTGCTCATCGCCCTCACAGCACCCAAAAAATCAGCAAC
CCAGGTTACCGGTCGCCACCATTACCTGGGGGGTTGTTTTGTGCCACCTGCTCTGGAAAAGAAGTAGCAGCTGAACCTGC
CC

Alignment

ORF - retro_pabe_2709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.48 %
• Parental protein coverage: 83.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QEEAQAVDQELFNEYQFSVDQLMELAGLSCATAIAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARHL
          QEEAQAVDQELFNEYQFSVD..MELAGLSCATAIAKA..PTSMSRSPPTVLVICGPG.NGGDGLVCA.HL
Retrocopy QEEAQAVDQELFNEYQFSVDRFMELAGLSCATAIAKACTPTSMSRSPPTVLVICGPGHNGGDGLVCAPHL

Parental  KLFG-YEPTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPSEPMMIDELYELVVDAIFGFSFKGDVRE-P
          KLFG...PTIYYPKRPNKPLF.ALVTQ.QK.DIPFLGEM.SEP.MI.ELYELVVDAIFGFSF.GDVRE..
Retrocopy KLFG>NQPTIYYPKRPNKPLFIALVTQGQKTDIPFLGEMRSEPVMI-ELYELVVDAIFGFSFEGDVRE<T

Parental  FHSILSVLKGLTVPIASIDIPSGWDVEKGNSGGIQPDLLISLTAPKKSATQFTGRYHYLGGRFVPPALEK
          FHSILSVLKGLTVPIA.I.IPSGWDVEKGNSGGIQPDLLI.LTAPKKSATQ.TGR.HYLGG.FVPPALEK
Retrocopy FHSILSVLKGLTVPIAGINIPSGWDVEKGNSGGIQPDLLIALTAPKKSATQVTGRHHYLGGCFVPPALEK

Parental  KYQLNLP
          K.QLNLP
Retrocopy K*QLNLP

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	0.28 RPM	20.29 RPM
SRP007412_cerebellum	0.12 RPM	17.27 RPM
SRP007412_heart	0.03 RPM	15.29 RPM
SRP007412_kidney	0.23 RPM	31.82 RPM
SRP007412_liver	0.03 RPM	18.51 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2709 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2709 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3275
Pan troglodytes	retro_ptro_2215
Gorilla gorilla	retro_ggor_2228
Macaca mulatta	retro_mmul_2060

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163382	2 retrocopies	retro_hsap_1973, retro_hsap_3275,
Gorilla gorilla	ENSGGOG00000000754	1 retrocopy	retro_ggor_2228,
Macaca mulatta	ENSMMUG00000002623	2 retrocopies	retro_mmul_1364, retro_mmul_2060,
Nomascus leucogenys	ENSNLEG00000012663	2 retrocopies	retro_nleu_2615, retro_nleu_2992,
Pongo abelii	ENSPPYG00000000713	2 retrocopies	retro_pabe_1692, retro_pabe_2709 ,
Pan troglodytes	ENSPTRG00000001463	2 retrocopies	retro_ptro_1315, retro_ptro_2215,