RetrogeneDB ID: retro_ggor_2112

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:118184071..118185094(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000179051
• Ensembl ID: ENSGGOG00000015263
• Aliases: None
• Description: None

Sequence

>retro_ggor_2112
CAGCTGGGACATGGGGACACCAAGAGAGTGGAAGCCCCCAGACTCATCGAGGGTCTCAGCCACAAAGTGATCGTATCTGC
AGCATGTGGGCAGAACCACACCTTGGCCTTGAGGGAAACTGGCTCCGTGTTTGCATTTGGGGAGAACAAGATGGGGCAGC
TGGGCCTTGGCAACCAGACAGACTGTCCACAGCCCCGCACAGATAATGTACAATGGCCAGCCAATTACCAAAATGGCCTG
TGGGGGCTGAATTCAGTATGATAATAGACTGCAGAGGAAACCTCTGTTCCTTTGGGTGCCCTGAATATGGTCAGCTGGGA
CACAACTCGGATGGGAAGTTCATTGCCTGGCCATAGCAGATAGAATACGACTGCAAACTGGTGCCCCTGCAAGTGGCCAT
CTTCATCGAGAAGACCAAAAATTGACAGATGCTGCCTGTACCAAATGTGGTTGTGCAAGATGTGGCCAGTGGCACTAACC
ACACTCTGGTTCTGGACTCCCAGAGGCAAGTCTTCTCTGGGGCTCCAGTGGCTATGGCTGGTTGGGCCATGCAGAGCAGA
AGGATGAGATGGTTCCCCGCCTGGTGAAGCTGTTTGACTTTTCTGTCCGTGGGGTGTCCCAGATCTATGCTGGTTACACC
TGCTTCTTTGCCATCAGTGAAGTGGGTGGTCTGTTTTTCTGGGGGTCACCAACACCTCCCATGAATCTACCGTGTACCCA
AAAGCAGTGCAGGACCTCTGTGGCTGGATAATATGGAGCCTGGCTTGTGGGAAGAGCAGCATCACTGTGGCCACCAATGA
GAGCACCATCAGCTGGGGCCCGTCGCCAACCTTCGGGGAACACGGCTATGGGGACCACAAGCCTAAGTCTTCCACTGCAG
CCCAAGAGGTGAAGACTCTGGATAGCATTTTCTCAGAGCAGGTCGCCAAGGGCTACTCACACACCTTGGTGATAGCAAGA
GACAAATGCTAGACCGAGAAAGAGAAGATCAAGAAACTGCCAGAATACAACCCCCCAACCCTC

Alignment

ORF - retro_ggor_2112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.92 %
• Parental protein coverage: 69.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QLGHGDTKRVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFAFGENKM-GQLGLGNQTDAVPSPAQI
          QLGHGDTKRVEAPRLIEGLSH.VIVSAACG.NHTLAL.ETGSVFAFGENKM.G...L......V.SPAQI
Retrocopy QLGHGDTKRVEAPRLIEGLSHKVIVSAACGQNHTLALRETGSVFAFGENKM>GSWALATR-QTVHSPAQI

Parental  MYNGQPITKMACG-AEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIEYDCELVPRRVAIFIEK
          MYNGQPITKMACG.AEFSMI.DC.GNL.SFGCPEYGQLGHNSDGKFIA....IEYDC.LVP..VAIFIEK
Retrocopy MYNGQPITKMACG>AEFSMIIDCRGNLCSFGCPEYGQLGHNSDGKFIAWP*QIEYDCKLVPLQVAIFIEK

Parental  TKDGQILPVPNVVVRDVACGANHTLVLDSQKRVFS-WGFGGYGRLGHAEQKDEMVPRLVKLFDFPGRGAS
          TK..Q.LPVPNVVV.DVA.G.NHTLVLDSQ..VFS.WG..GYG.LGHAEQKDEMVPRLVKLFDF..RG.S
Retrocopy TKN*QMLPVPNVVVQDVASGTNHTLVLDSQRQVFS<WGSSGYGWLGHAEQKDEMVPRLVKLFDFSVRGVS

Parental  QIYAGYTCSFAVSEVGGLFFWGA-TNTSRESTMYPKAVQDLCGWRIRSLACGKSSIIVAADESTISWGPS
          QIYAGYTC.FA.SEVGGLFFWG..TNTS.EST.YPKAVQDLCGW.I.SLACGKSSI.VA..ESTISWGPS
Retrocopy QIYAGYTCFFAISEVGGLFFWGS<TNTSHESTVYPKAVQDLCGWIIWSLACGKSSITVATNESTISWGPS

Parental  PTFGELVSRDHKPKSSTAAQEVKTLDGIFSEKVTMGYSHSLVTPRDKSETEKEKIKKLPEYNRQTL
          PTFGE....DHKPKSSTAAQEVKTLD.IFSE.V..GYSH.LV..RDK..TEKEKIKKLPEYN..TL
Retrocopy PTFGEHGYGDHKPKSSTAAQEVKTLDSIFSEQVAKGYSHTLVIARDKC*TEKEKIKKLPEYNPPTL

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	0.91 RPM	27.62 RPM
SRP007412_cerebellum	0.43 RPM	15.40 RPM
SRP007412_heart	0.16 RPM	6.16 RPM
SRP007412_kidney	1.19 RPM	24.66 RPM
SRP007412_liver	0.53 RPM	8.47 RPM
SRP007412_testis	1.45 RPM	25.49 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2112 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3073
Pan troglodytes	retro_ptro_2072
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,