RetrogeneDB ID: retro_ptro_1886

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:47012146..47013416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRC2
• Ensembl ID: ENSPTRG00000007871
• Aliases: None
• Description: cytochrome b-c1 complex subunit 2, mitochondrial [Source:RefSeq peptide;Acc:NP_001233459]

Sequence

>retro_ptro_1886
TTTTTGAGACTTTATTCCCTCAAAGTTGCCCCCAAAGTTAAAGCCACAGCTACCCCCACAGGAGTGGCTCCACATCATCA
GGACCTTGAGATCATCAAATTTCCAAATGGTTTTATGATTTCTCCTTTGGAAAACTATGCCCTGCATCAAGAATTGGTTT
GTTCATTAAAGCAGGCAGTAGCTATGAGGACTCCAACAATTTAGTAACTTCTCATTTGCTGTGTCTTGCATCCAGTTTGA
CTACAAAAGGAGCTTCATTTTTCAAGATAGCCCATGACGTTGAAGCAGCTGGTGGTAAATTAAGTGTAATTGCAACAAGA
GAAAACATAGCTTACATCATGGAATGTCTGCAGAGTGATATTGATATTCTAATGGAGTTCCTGCTCAGTGTCGCCACAGC
ACCAGGATTTGGTCATTGGGAAGTAGATGCCTTCAGTCTCAGCTAAGGATAGACAGAGCTGTGAATTTTCAGAATCCACA
GGCACATGTCATTGAAAATTTGCATACTGAAGCTTATTGGGATGCCTTGGCTAATTCCTTGTATTGTCCTGGCTATAGGA
TTGGAAAAGTGACATGGGAAGAGTTACATTACTATGTTTAGAACCACTTCACAAGTGCAAGAATGGCTTGGTTGGACTTG
GTGTGAGTCACCCTGTTCTAAAGCAAGTTGCTGAATAGTTTCTCAACAGGAGGGGTGGGTTTCTTTTGTCTGGTACAAAA
GCCAAATACTGTGGAGGTGAAATTCAGGAACAAAATGGAGACAGTCTTGTCCATGCTTGCTCTTGTAGCAGAAAGTGCTG
CCACAAGAAGGGCACAGCAAATGCATTTAGTGTTTTTCAGCATATCAAGAGGGACACCATATGTCAAGGGGCACAGTGAT
GCCACCAGCTATCTATAGCAGGCTATTGCCAAGGCAATTCACCAGCCACTTGCTATTTCTGTTTTTAATGCTAGTTACTC
CAATTTTGGACTCTTCAGGATGTACATTGTCTTCCAGGCTGCAGCTGCTGGAGATGTTATCAAGGCTGCCTATAACCAAG
TGGAAATAATTGCTCAAGAAAAGCTTTTCAATGTCCAGGCTGCCAAGAACAAACTGAAAGCTGGATACCAAATATAAGTG
AAGTCTTCTGAGGGTTTCATAGAAGAAGTCAGGCCCCAGGCTGTAGTTACTGGTTCTTACAAGCCAATATCACCAGTCCT
TCAGTAGATTAGTTGGTTGGCTAGTGCTGTCATCATCAATTCTGCAAAGAAGTTTGCTTCTGGCTAGAAA

Alignment

ORF - retro_ptro_1886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.52 %
• Parental protein coverage: 94.26 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FSRFYSLKVAPKVKATAAPAGAPPQPQDLEFTKLPNGLVIASLENYS-PISRIGLFIKAGSRYEDFNNLG
          F.R.YSLKVAPKVKATA.P.G..P..QDLE..K.PNG..I..LENY..P.SRIGLFIKAGS.YED.NNL.
Retrocopy FLRLYSLKVAPKVKATATPTGVAPHHQDLEIIKFPNGFMISPLENYA<PASRIGLFIKAGSSYEDSNNLV

Parental  TTHLLRLTSSLTTKGASSFKITRGIEAVGGKLSVTATRENMAYTVECLRGDVDILMEFLLNVTTAPEFRR
          T.HLL.L.SSLTTKGAS.FKI....EA.GGKLSV.ATREN.AY..ECL..D.DILMEFLL.V.TAP.F..
Retrocopy TSHLLCLASSLTTKGASFFKIAHDVEAAGGKLSVIATRENIAYIMECLQSDIDILMEFLLSVATAPGFGH

Parental  WEVAD-LQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTSEELHYFVQNHFTSAR
          WEV...LQ.QL.ID.AV.FQNPQ.HVIENLH..AY..ALAN.LYCP.YRIGKVT.EELHY.V.NHFTSAR
Retrocopy WEVDA<LQSQLRIDRAVNFQNPQAHVIENLHTEAYWDALANSLYCPGYRIGKVTWEELHYYV*NHFTSAR

Parental  MA-LIGLGVSHPVLKQVAEQFLNMRGGLGLSGAKANYRGGEIREQNGDSLVHA-AFVAESAVAGSAEANA
          MA.L.GLGVSHPVLKQVAE.FLN.RGG..LSG.KA.Y.GGEI.EQNGDSLVHA.A.VAESA....A....
Retrocopy MA<LVGLGVSHPVLKQVAE*FLNRRGGFLLSGTKAKYCGGEIQEQNGDSLVHA>ALVAESAATRRAQ-QM

Parental  FSVLQHVLGAGPHVKRGSNTTSHLHQAVAKATQQPFDVSAFNASYSDSGLFGIYTISQATAAGDVIKAAY
          ..V........P.VK..S..TS.L.QA.AKA..QP...S.FNASYS..GLF..Y...QA.AAGDVIKAAY
Retrocopy HLVFFSISRGTPYVKGHSDATSYL*QAIAKAIHQPLAISVFNASYSNFGLFRMYIVFQAAAAGDVIKAAY

Parental  NQVKTIAQGNLSNTDVQAAKNKLKAGYLMSVESSECFLEEVGSQALVAGSYVPPSTVLQQIDSVANADII
          NQV..IAQ..L.N..VQAAKNKLKAGY...V.SSE.F.EEV..QA.V.GSY.P.S.VLQ.I...A.A.II
Retrocopy NQVEIIAQEKLFN--VQAAKNKLKAGYQI*VKSSEGFIEEVRPQAVVTGSYKPISPVLQ*ISWLASAVII

Parental  NAAKKFVSGQK
          N.AKKF.SG.K
Retrocopy NSAKKFASG*K

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	111.09 RPM
SRP007412_cerebellum	0.00 RPM	137.37 RPM
SRP007412_heart	0.00 RPM	362.67 RPM
SRP007412_kidney	0.00 RPM	169.02 RPM
SRP007412_liver	0.00 RPM	85.60 RPM
SRP007412_testis	0.00 RPM	146.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1886 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1886 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2785
Gorilla gorilla	retro_ggor_1941

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886 ,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Vicugna pacos	ENSVPAG00000010914	1 retrocopy	retro_vpac_640,