RetrogeneDB ID: retro_ptro_2072

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:111399497..111400531(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCC2
• Ensembl ID: ENSPTRG00000000247
• Aliases: None
• Description: Regulator of chromosome condensation 2 [Source:UniProtKB/TrEMBL;Acc:K7ABL4]

Sequence

>retro_ptro_2072
AAGAAGGGGCAGCTGGGACATGGGGACACCAAGAGAGTGGAAGCCCCCAGACTCATCGAGGGTCTCAGCCACAAAGTGAT
CGTATCTGCAGCATGTGGGCAGAACCACACCTTGGCCTTGAGGGAAACTGGCTCCGTGTTTGCATTTGGGGAGAACAAGA
TGGGGCAGCTGGGCCTTGGCAACCAGACAGACACTGTCCACAGCCCCACGCAGAGAATGTACAACGGCCAGCCAATTACC
AAAATGGCCTGTGGGGGCTGAATTCAGTATGATAATAGACTGCAGAGGAAACCTCTGTTCCTTTGGGTGCCCTGAATATG
GTCAGCTGGGACACAACTCGGATGGGAAGTTCATTGCCTGGCCACAGCAGATAGAATACGACTGCAAACTGGTGCCCCTG
CAAGTGGCCATCTTCATCGAGAAGACCAAAAATTGACAGATGCTACCTGTACCAAACGTGGTTGTGCAAGATGTGGCCAG
TGGCACTAACCACACTCTGGTTCTGGACTCCCAGAAGCAAGTCTTCTCTGGGGCTCCAGTGGCTATGGCTGGCTGGGCCA
TGCAGAGCAGAAGGATGAGATGGTCCCCCGCCTGGTGAAGCTGTTTGACTTTTCTGGATGTGGGGTGTCCCAGATCTATG
CTGGTTACACCTGCTTCTTTGCCATCAGTGAAGTGGGTGGTCTGTTTTTCTGGGGGTCACCAACACCTCCCACGAATCTA
CTGTGTACCCGAAAGCAGTGCAGGACCTCAGTGGCTGGAGAATACGGAGCCTGGCTTGTGGGAAGAGCAGCGTCACTGTG
GCCACCAATGAGAGCACCATCAGCTGGGGCCCGTCGCCGACCTTCGGGGAACACGGCTATGGGGACCACAAGCCCAAGTC
TTCCACTGCAGCCCAAGAGGTGAAGACTGTGGATAGCATTTTCTCAGAGCAGGTCGCCAAGGGCTACTCACACACCTTGG
TGATAGCAAGAGACAAATGCTAGACCGAGAAAGAGAAGATCAAGAAACTGCCAGAACACAACCCCCCAACCCTC

Alignment

ORF - retro_ptro_2072 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.77 %
• Parental protein coverage: 80.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKGQLGHGDTKRVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFAFGENKMGQLGLGNQTDAVPSPA
          .KGQLGHGDTKRVEAPRLIEGLSH.VIVSAACG.NHTLAL.ETGSVFAFGENKMGQLGLGNQTD.V.SP.
Retrocopy KKGQLGHGDTKRVEAPRLIEGLSHKVIVSAACGQNHTLALRETGSVFAFGENKMGQLGLGNQTDTVHSPT

Parental  QIMYNGQPITKMACG-AEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIEYDCELVPRRVAIFI
          Q.MYNGQPITKMACG.AEFSMI.DC.GNL.SFGCPEYGQLGHNSDGKFIA..Q.IEYDC.LVP..VAIFI
Retrocopy QRMYNGQPITKMACG>AEFSMIIDCRGNLCSFGCPEYGQLGHNSDGKFIAWPQQIEYDCKLVPLQVAIFI

Parental  EKTKDGQILPVPNVVVRDVACGANHTLVLDSQKRVFS-WGFGGYGRLGHAEQKDEMVPRLVKLFDFPGRG
          EKTK..Q.LPVPNVVV.DVA.G.NHTLVLDSQK.VFS.WG..GYG.LGHAEQKDEMVPRLVKLFDF.G.G
Retrocopy EKTKN*QMLPVPNVVVQDVASGTNHTLVLDSQKQVFS<WGSSGYGWLGHAEQKDEMVPRLVKLFDFSGCG

Parental  ASQIYAGYTCSFAVSEVGGLFFWGA-TNTSRESTMYPKAVQDLCGWRIRSLACGKSSIIVAADESTISWG
          .SQIYAGYTC.FA.SEVGGLFFWG..TNTS.EST.YPKAVQDL.GWRIRSLACGKSS..VA..ESTISWG
Retrocopy VSQIYAGYTCFFAISEVGGLFFWGS<TNTSHESTVYPKAVQDLSGWRIRSLACGKSSVTVATNESTISWG

Parental  PSPTFGELGYGDHKPKSSTAAQEVKTLDGIFSEQVAMGYSHSLVIARDESETEKEKIKKLPEYNPRTL
          PSPTFGE.GYGDHKPKSSTAAQEVKT.D.IFSEQVA.GYSH.LVIARD...TEKEKIKKLPE.NP.TL
Retrocopy PSPTFGEHGYGDHKPKSSTAAQEVKTVDSIFSEQVAKGYSHTLVIARDKC*TEKEKIKKLPEHNPPTL

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	42.93 RPM
SRP007412_cerebellum	0.00 RPM	36.67 RPM
SRP007412_heart	0.00 RPM	11.08 RPM
SRP007412_kidney	0.21 RPM	37.42 RPM
SRP007412_liver	0.00 RPM	32.90 RPM
SRP007412_testis	0.11 RPM	30.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2072 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2072 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3073
Gorilla gorilla	retro_ggor_2112
Pongo abelii	retro_pabe_2547

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001396	1 retrocopy	retro_dnov_2692,
Homo sapiens	ENSG00000179051	3 retrocopies	retro_hsap_2677, retro_hsap_3073, retro_hsap_3597,
Gorilla gorilla	ENSGGOG00000015263	1 retrocopy	retro_ggor_2112,
Nomascus leucogenys	ENSNLEG00000007783	2 retrocopies	retro_nleu_2483, retro_nleu_298,
Otolemur garnettii	ENSOGAG00000014544	1 retrocopy	retro_ogar_2967,
Pongo abelii	ENSPPYG00000025834	3 retrocopies	retro_pabe_2547, retro_pabe_2957, retro_pabe_748,
Pan troglodytes	ENSPTRG00000000247	3 retrocopies	retro_ptro_1804, retro_ptro_2072 , retro_ptro_2434,
Rattus norvegicus	ENSRNOG00000006327	1 retrocopy	retro_rnor_1378,