RetrogeneDB ID: retro_ptro_2603

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:22181985..22183778(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCE1
• Ensembl ID: ENSPTRG00000016481
• Aliases: None
• Description: Pan troglodytes ATP-binding cassette, sub-family E (OABP), member 1 (ABCE1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246609]

Sequence

>retro_ptro_2603
CTAGCAGACAAATTAATGAGAATTGCTATTGTCAATCATGACAAATGTAAACCTAAGAAATGTCAACAGGAATGCAGAAA
GAGTTGTCCTGTAGTTCAAATGGGAGAATTATGCATAGAAGTTACACTCCAGAACAAAATAGCATGGATTTCTGAAACTC
TTTGTATTGGTTGTGGTATCTGTATTAAGAAATGCCCCTTTGGCGCCTTATCAATTGACAATTTACCAAGCAACTTGGAA
AAAGAAACCACACATTGATATTGTGCCAATGTCATCTAAATTCACAGTTGCCTATCCCTCGTCCAGGTAAAGTTTTGGGA
TTAGTTGGAACTAATGGTATTGGAAAGTCAACTGCTTTAAAAATTTTTAGCAGGAAAACAAAAGCCAAACCTTGGAAAGT
ACGATGATCCTCCTGACTGGCAAGACATTTTGACTTATTTCCGTGAATCTGAATTACAGAATTACTTTACCAAGATTCTA
GAAGAGAACCTAAAAGCCATCATCAAATCTCAATATGTAGACCAGATTCCTAAGCCTGCAAAGGGGACAGTGGGATCTAT
TTTGGACTGAAAAGATGAAACAAAGACACAGGCAATTGTATGTCAGCAGCTTGAATTAACCCACCTAACAGAACGAAATG
TTGAAGATCTTTCAGGAGGAGAGTTGCAGAGATTTGCCTGTGCTGTCATTTGCATACAGAAAGCTGATATTTTCATGTTT
GGTGAGACTTCTAGTTACCTAGATGTCAAACAGCATTTAAAGCCTGCTATTACTATACAATCTCTGATAAATCCAGACAG
ATATATCATTGTAGTGGAATATGATCTAGGTGTATTAGACTATCTCTCTGATTTCAACTGCTGTTTATATGGTGTACCAA
GCACCTATGGAGTTGTCACTGTGCCTTTTAGTGTAAGAAAGGGCATAAACATTTTTTTGGATGGCTATGTTCCAACAGAA
AACTTGAGATTCCAAGATGCATCACTTGTTTTTAAAGTGGCTGAGACAGCAAATGAAGAAGAAGTCAAAATGATGTGTAT
GTATAAATATTCAGGAATGAATTAAAAATGGGAGAGTTTGAGCTAGCAATTGTAGCTGGAGAGTTTACAGATTCTGAAAT
CATGGTGATGATGCTAGGGGAAAATGGAATGGGTAAAACGACATTTATCAGAATGCTTGCTGGAAGACTTAAACCTGATG
AAGAAGAAGTACCAGTTCTAAATGTCAGTTATAAGTTACAGAAAATTAGTCCCAAATTAACTGGAAGTGTTCGCCAGTTA
CTACATGAAAAAATAAGAGATGCTTATACACATCCACAATTTGTGACTAATGTAATGAAGCCTCTGCAAATTGAAAACAT
CATCGATCAAGAGGTGCAGACATTATCGGGTGGTGAACTACAGCGAGTAGCTTTAGCCCTTTGTTTGGGCAAACCTGCTG
ATGTCTATTTAATTGATGAACCATCTGCATATTTGGATTCTGAGCAAAGACTGATGGCAGCTCGAGTTGTCAAACGTTTC
ATACTTCATGCAAAAAAGACAGCCTTTGTTGTGGAACATGACTTCATCATGGCCACCTATCTAGCGGATCATGTCATCAT
TTTTTATGGTCTTCCATCTACTAAGAACACAGTTGCAAACAGTCCTCAAACCCTTTTGGCTGGCATGAATACATTTTAGT
CTCAGCTTGAAACTACATTCAGAAGAGATCCAAACCACTATAGACCACGAATAAATAAATTTAATTTAATTAAGGATGTA
GAACAAAAGAAGAGTGGAAACTACTTTTTCTTG

Alignment

ORF - retro_ptro_2603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.53 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGICIKKCPFGAL
          .ADKL.RIAIVNHDKCKPKKC.QEC.KSCPVV.MG.LCIEVT.Q.KIAWISETLCIGCGICIKKCPFGAL
Retrocopy LADKLMRIAIVNHDKCKPKKCQQECRKSCPVVQMGELCIEVTLQNKIAWISETLCIGCGICIKKCPFGAL

Parental  SIVNLPSNLEKETTHRYCANAFKLH-RLPIPRPGEVLGLVGTNGIGKSTALKI-LAGKQKPNLGKYDDPP
          SI.NLPSNLEKETTH.YCAN....H..LPIPRPG.VLGLVGTNGIGKSTALKI.LAGKQKPNLGKYDDPP
Retrocopy SIDNLPSNLEKETTH*YCANVI*IH<QLPIPRPGKVLGLVGTNGIGKSTALKI>LAGKQKPNLGKYDDPP

Parental  DWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQLDLTH
          DWQ.ILTYFR.SELQNYFTKILE..LKAIIK.QYVDQIPK.AKGTVGSILD.KDETKTQAIVCQQL.LTH
Retrocopy DWQDILTYFRESELQNYFTKILEENLKAIIKSQYVDQIPKPAKGTVGSILD*KDETKTQAIVCQQLELTH

Parental  LKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRLKAAITIRSLINPDRYIIVVEHDLSV
          L.ERNVEDLSGGELQRFACAV.CIQKADIFMF.E.SSYLDVKQ.LK.AITI.SLINPDRYIIVVE.DL.V
Retrocopy LTERNVEDLSGGELQRFACAVICIQKADIFMFGETSSYLDVKQHLKPAITIQSLINPDRYIIVVEYDLGV

Parental  LDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMCMY
          LDYLSDF.CCLYGVPS.YGVVT.PFSVR.GINIFLDGYVPTENLRF.DASLVFKVAETANEEEVK.MCMY
Retrocopy LDYLSDFNCCLYGVPSTYGVVTVPFSVRKGINIFLDGYVPTENLRFQDASLVFKVAETANEEEVKMMCMY

Parental  KYPGM-KKKMGEFELAIVAGEFTDSEIMV-MLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQKI
          KY.GM...KMGEFELAIVAGEFTDSEIMV.MLGENG.GKTTFIRMLAGRLKPDE..EVPVLNVSYK.QKI
Retrocopy KYSGM<ELKMGEFELAIVAGEFTDSEIMVMMLGENGMGKTTFIRMLAGRLKPDE-EEVPVLNVSYKLQKI

Parental  SPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID
          SPK.TGSVRQLLHEKIRDAYTHPQFVT.VMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID
Retrocopy SPKLTGSVRQLLHEKIRDAYTHPQFVTNVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID

Parental  EPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADRVIVFDGVPS-KNTVANSPQTLLAGM
          EPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLAD.VI.F.G.PS.KNTVANSPQTLLAGM
Retrocopy EPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADHVIIFYGLPSTKNTVANSPQTLLAGM

Parental  NKFLSQLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFL
          N.F.SQLE.TFRRDPN.YRPRINK.N.IKDVEQKKSGNYFFL
Retrocopy NTF*SQLETTFRRDPNHYRPRINKFNLIKDVEQKKSGNYFFL

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	0.02 RPM	21.31 RPM
SRP007412_cerebellum	0.00 RPM	27.82 RPM
SRP007412_heart	0.00 RPM	24.57 RPM
SRP007412_kidney	0.00 RPM	22.46 RPM
SRP007412_liver	0.00 RPM	19.12 RPM
SRP007412_testis	0.00 RPM	39.10 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2603 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2603 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2603 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3826
Pongo abelii	retro_pabe_3067

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925, retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603 ,