RetrogeneDB ID: retro_pabe_2232

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:100247078..100247939(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRC2
• Ensembl ID: ENSPPYG00000007174
• Aliases: None
• Description: ubiquinol-cytochrome c reductase core protein II [Source:HGNC Symbol;Acc:12586]

Sequence

>retro_pabe_2232
ATGAGGCTACTGACCAGAGCTGGGTTCTTTTTGAGACTTTATTCCCTCAAAGTTGCCCCCAAAGTTAAAGCCACAGCTAC
CCCCACAGGAGAGGCTCCACATCATCAGGACCTTGAGATCATCAAATTTCCAAGTGGTTTTGTGATTTCTCCTTTGGAAA
ACTATGCTCTGCATCAAGAATTGGTTTGTTCATTAAAGCAGGCAGTAGCTATGAGGACTCCAACAATTTAGTAACTTCTC
ATTTGCTGTGTCTTTCATCCAGTTTGACTACGAAAGGAACTTCATCTTTCAAGATAGCCCATGACATTGAAGCAGCTGGT
GGTAAATTAAGTGTAATTGCAACAAGAGAAAACATAGCTTACATCATGGAATGTCTGCAGAGTGATATTGATATTCTAAT
GGAGTTCCTGCTCAATGTCGCCACAGCACCAGGATTTTATCATTGGGAAGTAGCTGCCTTCAGTCTCAGCTAATGATAGA
CAAAGCTGTGAATTTTCAGAATCCACAGGCACATGTCATTGAAAATTTGCATACTGAAGCTTATTGGGATGCCTTGGCTA
ATTCCTTGTATTGTCCTGGCTATAGGATTGGAAAAGTGACATGGGAAGAGTTACATTACTGTGTTTAGAACCACTTCACA
AGTGCAAGAATGGCTTGGTTGGACTTGGTGTGAGTCACTCTGTTCTAAAGCAAGTTGCTGAATAGTTTCTCAACAGGAGG
GGTGGGTTTCTTTCATCTGGTACAAAAGCCAAATACTGTGGAGGTGAAATTCAAGAACAAAATGGAGACAGTCTTGTCCA
TGCTTGCTCTTGTAGCAGAAAGTGCTGCCACAAGATGGGCACAGCAAATGCATTTAGCATA

Alignment

ORF - retro_pabe_2232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 63.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MKLLTRAGSFSRFYSLKVAPKVKATAVPAGAPPQPQDLEFTKLPNGLVIASLENYA-PISRIGLFIKAGS
          M.LLTRAG.F.R.YSLKVAPKVKATA.P.G..P..QDLE..K.P.G.VI..LENYA...SRIGLFIKAGS
Retrocopy MRLLTRAGFFLRLYSLKVAPKVKATATPTGEAPHHQDLEIIKFPSGFVISPLENYA<SASRIGLFIKAGS

Parental  RYEDSNNLGTTHLLRLTSSLTTKGASSFKITRGIEAVGGKLSVTATRENMAYTVECLRGDVDILMEFLLN
          .YEDSNNL.T.HLL.L.SSLTTKG.SSFKI...IEA.GGKLSV.ATREN.AY..ECL..D.DILMEFLLN
Retrocopy SYEDSNNLVTSHLLCLSSSLTTKGTSSFKIAHDIEAAGGKLSVIATRENIAYIMECLQSDIDILMEFLLN

Parental  VTTAPEFRRWEVAN-LQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTSEELHYF
          V.TAP.F..WEVA..LQ.QL.IDKAV.FQNPQ.HVIENLH..AY..ALAN.LYCP.YRIGKVT.EELHY.
Retrocopy VATAPGFYHWEVAA<LQSQLMIDKAVNFQNPQAHVIENLHTEAYWDALANSLYCPGYRIGKVTWEELHYC

Parental  VQNHFTSARMA-LIGLGVSHPVLKQVAEQFLNMRGGLGLSGAKAKYRGGEIREQNGDSLVHA-AFVAESA
          V.NHFTSARMA.L.GLGVSH.VLKQVAE.FLN.RGG...SG.KAKY.GGEI.EQNGDSLVHA.A.VAESA
Retrocopy V*NHFTSARMA<LVGLGVSHSVLKQVAE*FLNRRGGFLSSGTKAKYCGGEIQEQNGDSLVHA>ALVAESA

Parental  VVGSAE-ANAFSV
          ....A..ANAFS.
Retrocopy ATRWAQ<ANAFSI

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	119.21 RPM
SRP007412_cerebellum	0.00 RPM	122.94 RPM
SRP007412_heart	0.00 RPM	231.04 RPM
SRP007412_kidney	0.00 RPM	142.63 RPM
SRP007412_liver	0.00 RPM	101.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2232 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2232 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1442

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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,