RetrogeneDB ID: retro_pabe_2288

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:12347074..12348317(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTOV1
• Ensembl ID: ENSPPYG00000010265
• Aliases: None
• Description: prostate tumor overexpressed 1 [Source:HGNC Symbol;Acc:9632]

Sequence

>retro_pabe_2288
ATGGTCCGTCCGCGCCGGGCCCCGTACCGCTCCGGCGCCGGGGGCCCCCTCGGGGGTCACGGCCGCCCCGCGCGCCCCTC
ATAGTGCGCGCTTTCGGCTCGCGCTCCTGGCCCGCCAGCCCCCAAGGCCCGCAGCCTCTGCAGATCCAGGCCTGCTCGGC
TCCTCCCATGGAAGGTGCTCGGGTCTTCGGGGCGCTGGGTCCCATCGGTCCCTCCTCACCTGGGCTCACCCTCGGGGGCC
TGGCCGTGAGCGAGCACCGGCTCAGCAACAAGCTGCTGGCCTGGAGCGGCGTCCTCGAGTGACAGGAGAAGCGCAGACCC
TACTGTGACTCCACTGTAAAGTTGAGGCGGACCCTGCCCTGCCAAGCCTCCGTGAACCAAGGCGAGAACCTGGAGCCCAA
CCAGTGGCAGCAGAAGCTGATCATGCAGCTGATCCCGCAGCAGCTAATGAGCACGCTGGGACCCCTGTTCCGCAACTCCC
AGCTGGCACAGTTCCACTTCACCAACAGAGACTGCGGCTTGCTCAGTGGGCTCTGCCGCATCATGGGCAACGGCTTCGCG
GGCTGCATGCTGTTCCCCCACATCTCCCGCTGCGAGATGTGCGTGCTCATGCTCCTGTACTCTTCCAAGAGGAAGATCTT
CATGGGCTTCATCCCCTACGACCGGAGCGGTTTCGTTAGCGCCATTCGGCAGGTCATCACTACCCGCAAGCAAGCAGTGG
GACCTGGTGGTGTCAACTCAGGCCCAGTCCAGATCGTCAACAAGTTCCTGGCGTGGAGCGGCGTCATGGAGTGGCAGGAA
CCCAGGCCTGAGCCCAAAAGTCGGTCCAAGAGGTGGCTGCCGTCCCATGTCTACGTGAACCAGGGGGAGATCCTGAGGAC
CGAGCAGTGGCCGAGGAAGCTGTACATGCAGCTCATCCCGCAGCAGCTGCTGACCACCCTGTGCTGCTGTTGCGGAACTC
GCGCCTGGTGCAGTTCCACTTCACCAAGGACCTGGAGACGCTGAAGAGCCTGTGCCAGATCATGGACAATGGCTTCGCCG
GCTGAGTGCATTTTTCCTACAAAGCGTTGTGCGAGATCCGTGTGCTTATGCTCCTATACTCCTCTGAGAAGAAAATCTTC
ATCGGCCTCATCCTCCGTGACCAAGGCAACTTCCTCAACGGCATACGGCGAGTCATTGCCAACTAGCAGCAGGTCCTGCA
GCGGAACCTGGAGCAGGAGCAGCAGCAGCAAGGAATGGAGGGT

Alignment

ORF - retro_pabe_2288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVRPRRAPYRSGAGGPLGGRGRPPRP-LVVRAVRSRSWPASPRGPQPPRIRARSAPPMEGARVFGALGPI
          MVRPRRAPYRSGAGGPLGG.GRP.RP.L.VRA..SRSWPASP.GPQP..I.A.SAPPMEGARVFGALGPI
Retrocopy MVRPRRAPYRSGAGGPLGGHGRPARP<LIVRAFGSRSWPASPQGPQPLQIQACSAPPMEGARVFGALGPI

Parental  GPSSPGLTLGGLAVSEHRLSNKLLAWSGVLEWQEKRRPYSDSTAKLKRTLPCQAYVNQGENLETDQWPQK
          GPSSPGLTLGGLAVSEHRLSNKLLAWSGVLE.QEKRRPY.DST.KL.RTLPCQA.VNQGENLE..QW.QK
Retrocopy GPSSPGLTLGGLAVSEHRLSNKLLAWSGVLE*QEKRRPYCDSTVKLRRTLPCQASVNQGENLEPNQWQQK

Parental  LIMQLIPQQLLTTLGPLFRNSQLAQFHFTNRDCDSLKGLCRIMGNGFAGCMLFPHISPCEVRVLMLLYSS
          LIMQLIPQQL..TLGPLFRNSQLAQFHFTNRDC..L.GLCRIMGNGFAGCMLFPHIS.CE..VLMLLYSS
Retrocopy LIMQLIPQQLMSTLGPLFRNSQLAQFHFTNRDCGLLSGLCRIMGNGFAGCMLFPHISRCEMCVLMLLYSS

Parental  KKKIFMGLIPYDQSGFVSAIRQVITTRKQAVGPGGVNSGPVQIVNNKFLAWSGVMEWQEPRPEPNSRSKR
          K.KIFMG.IPYD.SGFVSAIRQVITTRKQAVGPGGVNSGPVQIV.NKFLAWSGVMEWQEPRPEP.SRSKR
Retrocopy KRKIFMGFIPYDRSGFVSAIRQVITTRKQAVGPGGVNSGPVQIV-NKFLAWSGVMEWQEPRPEPKSRSKR

Parental  WLPSHVYVNQGEILRTEQWPRKLYMQLIPQQLLTTL-VPLFRNSRLVQFHFTKDLETLKSLCRIMDNGFA
          WLPSHVYVNQGEILRTEQWPRKLYMQLIPQQLLTTL.V.L.RNSRLVQFHFTKDLETLKSLC.IMDNGFA
Retrocopy WLPSHVYVNQGEILRTEQWPRKLYMQLIPQQLLTTL<VLLLRNSRLVQFHFTKDLETLKSLCQIMDNGFA

Parental  GCVHFSYKASCEIRVLMLLYSSEKKIFIGLIPHDQGNFVNGIRRVIANQQQVLQRNLEQEQQQRGMGG
          G.VHFSYKA.CEIRVLMLLYSSEKKIFIGLI..DQGNF.NGIRRVIAN.QQVLQRNLEQEQQQ.GM.G
Retrocopy G*VHFSYKALCEIRVLMLLYSSEKKIFIGLILRDQGNFLNGIRRVIAN*QQVLQRNLEQEQQQQGMEG

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	0.00 RPM	59.05 RPM
SRP007412_cerebellum	0.00 RPM	62.38 RPM
SRP007412_heart	0.00 RPM	21.83 RPM
SRP007412_kidney	0.03 RPM	58.77 RPM
SRP007412_liver	0.00 RPM	33.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2288 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2288 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2694
Pan troglodytes	retro_ptro_1818
Gorilla gorilla	retro_ggor_1877
Macaca mulatta	retro_mmul_1426

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003495	1 retrocopy	retro_cfam_289,
Callithrix jacchus	ENSCJAG00000004105	1 retrocopy	retro_cjac_445,
Homo sapiens	ENSG00000104960	1 retrocopy	retro_hsap_2694,
Gorilla gorilla	ENSGGOG00000010182	1 retrocopy	retro_ggor_1877,
Macaca mulatta	ENSMMUG00000011618	1 retrocopy	retro_mmul_1426,
Nomascus leucogenys	ENSNLEG00000005374	1 retrocopy	retro_nleu_1191,
Pongo abelii	ENSPPYG00000010265	1 retrocopy	retro_pabe_2288 ,
Pan troglodytes	ENSPTRG00000011321	1 retrocopy	retro_ptro_1818,