RetrogeneDB ID: retro_pabe_190

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:90089549..90090698(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020526
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSPPYG00000001506
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_pabe_190
ATGGGGAGCGGGGAGCCTAATCCTGCTGGCAAGAAAAAGAAGTATCTCAAGGCCGCTCTGTACGTGGGTGACTTGGACCC
AGATGTCACCGAGGACATGCTCTATAAGAAGTTCAGGCCTGCTGGCCCTCTGCGATTCACCCGAATCTGCCGTGATCCGG
TGACCCGCAGCCCCCTGGGCTATGGGTATGTTAACTTCCGCTTTCCCGCGGATGCAGAGTGGGCCTTGAACACCATGAAT
TTTGATTTGATTAATGGAAAACCATTCCGCCTTATGTGGTCTCAGCCAGATGACCGCTTAAGAAAGTCTGGAGTGGGAAA
TATATTCATCAAAAACCTGGACAAATCCATAGACAATAGGGCCCTGTTTTACTTATTTTCTGCTTTTGGGAACATTCTGT
CCTGCAAAGTCGTATGCGATGACAACGGCTCTAAGGGTTATGCCTATGTGCACTTTGACAGCCTGGCCGCTGCCAATAGA
GCCATCTGGCACATGAATGGAGTGCGGCTCAACAACCGCCAGGTGTATGTTGGCAGATTCAAATTCCCAGAAGAGCGGGC
GGCTGAGGTCAGAACCAGGGATAGAGCAACTTTCACCAATGTTTTCGTTAAAAACATTGGAGACGACATAGATGACGAAA
AACTGAAGGAACTTTTCTGTGAATATGGGCCAACTGAGAGTGTTAAAGTAATAAGAGATGCCAGTGGGAAATCTAAAGGC
TTTGGATTTGTGAGATATGAGACACACGAGGCTGCCCAAAAGGCTGTGCTAGACTTGCATGGAAAGTCCATCGATGGAAA
AGTCCTCTATGTAGGGCGAGCACAGAAGAAAATTGAACGCCTGGCTGAGTTGAGGCGGAGATTTGAACGGCTGAGGTTAA
AAGAAAAAAGTCGGCCCCCAGGGGTGCCTATCTATATTAAGAACTTGGATGAGACAATCAATGATGAAAAACTGAAGGAG
GAATTTTCTTCCTTTGGGTCAATTAGTCGGGCCAAAGTGATGATGGAAGTGGGGCAAGGCAAAGGATTTGGTGTGGTCTG
CTTTTCCTCTTTTGAAGAGGCTACCAAAGCAGTGGATGAGATGAATGGCCGCATAGTGGGCTCCAAGCCCCTGCATGTCA
CCCTGGGCCAGGCCAGGCGCAGGTGCTGA

Alignment

ORF - retro_pabe_190 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.58 %
• Parental protein coverage: 55.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
          Y..A.LYVGDL..DVTE.MLY.KF.PAGP....R.CRD..TR..LGY.YVNF..PADAE.AL.TMNFD.I
Retrocopy YLKAALYVGDLDPDVTEDMLYKKFRPAGPLRFTRICRDPVTRSPLGYGYVNFRFPADAEWALNTMNFDLI

Parental  KGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFET
          .GKP.R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN.AL...FSAFGNILSCKVVCD.NGSKGYA.VHF..
Retrocopy NGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRALFYLFSAFGNILSCKVVCDDNGSKGYAYVHFDS

Parental  QEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAK-EFTNVYIKNFGEEVDDESLKELFSQFGK
          ..AA..AI..MNG..LN.R.V.VGRFK...ER.AE........FTNV..KN.G...DDE.LKELF...G.
Retrocopy LAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTRDRATFTNVFVKNIGDDIDDEKLKELFCEYGP

Parental  TLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKFEQLKQE
          T.SVKV.RD..GKSKGFGFV.YE.HE.A.KAV....GK.I.GK...VGRAQKK.ER.AEL.R.FE.L...
Retrocopy TESVKVIRDASGKSKGFGFVRYETHEAAQKAVLDLHGKSIDGKVLYVGRAQKKIERLAELRRRFERLRLK

Parental  RISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGR
          ..SR..GV..YIKNLD.TI.DEKL..EFS.FGSI..AKVM.E.G..KGFG.VCFSS.EEATKAV.EMNGR
Retrocopy EKSRPPGVPIYIKNLDETINDEKLKEEFSSFGSISRAKVMMEVGQGKGFGVVCFSSFEEATKAVDEMNGR

Parental  IVGSKPLYVALAQRK
          IVGSKPL.V.L.Q..
Retrocopy IVGSKPLHVTLGQAR

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	0.66 RPM	41.19 RPM
SRP007412_cerebellum	1.22 RPM	37.70 RPM
SRP007412_heart	0.27 RPM	108.43 RPM
SRP007412_kidney	0.56 RPM	63.77 RPM
SRP007412_liver	0.03 RPM	73.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_190 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_190 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Macaca mulatta	ENSMMUG00000007497	1 retrocopy	retro_mmul_178,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000000562	2 retrocopies	retro_ocun_153, retro_ocun_792,
Otolemur garnettii	ENSOGAG00000004067	1 retrocopy	retro_ogar_71,
Ochotona princeps	ENSOPRG00000011984	1 retrocopy	retro_opri_1133,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190 , retro_pabe_2563,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,