RetrogeneDB ID: retro_pabe_1692

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19_random:4159053..4159503(+)
• 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_1692
GTCCCGATCATCCATGGCCCAGGGAATAATGGAGAAGGTAGCCTGCTCTGTGCCTGACACCCCAAACATTTTGGTCACCA
GCCAATCATCTTTGACCCCAAAAGACCCAACAAGCCACCCTACACTATGCTGGTGACCCACCGTCAGGAAAGGGGCATTC
TTTTGCTTGGTGAAATGCCCCCAGAGCCCATGCTGATCAATGAGCTATATGGGCTGGGGGTGGATGCCATCTTTGGCTTC
AGCTTCAAGGGCAATGTTTGAAAGCCATTCTGTAACATTCTGAGTGTCCTGAATGGACTCACTATGCCACTGCCAATGCT
GACATTCCCTTGGGATGGGACATGGAGAAGGAAAACTCTGGAGGGATCCAGCCAGACCGGCTTCTCTCCCTGATAGCACC
CAAAAAGTCTGAAACAGTAGTTTACAGATTGCTACCACTACTTGAGGGGT

Alignment

ORF - retro_pabe_1692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.13 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLVICGPGNNGGDGLVCARHLKLFGYEPTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPSEPMMIDELY
          V..I.GPGNNG...L.CA.H.K.FG..P.I..PKRPNKP..T.LVT..Q...I..LGEMP.EPM.I.ELY
Retrocopy VPIIHGPGNNGEGSLLCA*HPKHFGHQPIIFDPKRPNKPPYTMLVTHRQERGILLLGEMPPEPMLINELY

Parental  ELVVDAIFGFSFKGDVREPFHSILSVLKGLTVPI-ASIDIPSGWDVEKGNSGGIQPDLLISLTAPKKSAT
          .L.VDAIFGFSFKG.V..PF..ILSVL.GLT.P..A..DIP.GWD.EK.NSGGIQPD.L.SL.APKKS.T
Retrocopy GLGVDAIFGFSFKGNV*KPFCNILSVLNGLTMPL<ANADIPLGWDMEKENSGGIQPDRLLSLIAPKKSET

Parental  Q-FTGRYHYLGG
          ..FT..YHYL.G
Retrocopy V>FTDCYHYLRG

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	0.11 RPM	20.29 RPM
SRP007412_cerebellum	0.00 RPM	17.27 RPM
SRP007412_heart	0.00 RPM	15.29 RPM
SRP007412_kidney	0.03 RPM	31.82 RPM
SRP007412_liver	0.09 RPM	18.51 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1692 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1692 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1692 has 0 orthologous retrocopies within eutheria group .

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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,