RetrogeneDB ID: retro_ogar_2967

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873690.1:830218..831778(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCC2
• Ensembl ID: ENSOGAG00000014544
• Aliases: None
• Description: regulator of chromosome condensation 2 [Source:HGNC Symbol;Acc:30297]

Sequence

>retro_ogar_2967
ATGCCCAGGAAGGAGGCGGCGGCAGCGGCCTGGGAGGAGCCGAGCTCGGGCAACGGTACGGCCCGCGCCGGGCCCAGAAA
ACGCGGCGGCCTGGCGGGCAGGAAGCGCGAGCGACCGGAGCGCTGCAGTAGCAGCAGCAGCGGCGGCGGCGACGAGGACG
GTCTGGAGCTCGACGGGGCCCCCGGAGGGGGCAAGTGCGCGGCACGGCCGGCGGCGGCGGGCAAGGCTGGCGGCGCGGCT
GTGGTCGTCACTGAGCCCGAACACACCAAGGAGCGCGTCAAACTTGAAGGGTCGAAGTGCAAAGGGCAGCTTTTGATTTT
GGGGGCAACCAACTGGGACTTGATTGGTCAGAAAGAAGTGCCTAAACAGCAAGCCGCTTACCGCAATCTTGGGCAGAATC
TGTGGGGGCCCCACAGGTATGGGTGCCTGGCGGGAGTCCGGGTGCGGACGGTGGTCTCGGGCTCGTGTGCTGCGCACAGC
CTCCTCATCACCACAGAAGGGAAGCTGTGGAGCTGGGGTCGAAATGAGAAGGGGCAGCTGGGACATGGTGACACCAAGAG
AGTGGAAGCCCCCAGACTCATTGAGGGTCTCAGCCATGAAGTGATCGTGTTGGCAGCATGTGGGCGGAACCACACCCTGG
CCTTGACTGAAACCGGCTCCGTGTTTGCGTTTGGGTAGAACAAGATGGGGCAACTGGGCCTCGGCAACCAGACAGATGCC
GTCCCCAGCCCGGCTCAGATAGTGTACAGCGGCCAGCCAATTACCAAAATGGCCTGTGGGGCTGAATTCAGTATGATAAT
GGACTGCAAAGGAAACCTCTATTCCTTTGGGTGCCCTGAATATGGTCAGCTGGGACACAACTCGATGGGAAGTTCATTGC
CTGGGCGCAGCGGATAGAGTACGACTGTGAGCTGGTACCCCGGAGAGTGGCCATCTTCATTGAGAAGACGAAAGATGGGC
AGATTCTGCCCGTACCAAACGTGGTTGTTCGAGACATGGCCTGTGGCGCTAACCACACACTGGTCCTGGACTCCCAGAAG
CGAGTCTTCTCTTGGGGCTTTAGTGGCTATGGCCGGCTCGGCCACGCGGAGCAGAAGGATGAGATGGTCCCTCGCCTGGT
GAAGCTGTTTGATTTCCCTGATCGTGGGGCGTCCCAGATCTACGCTGGTTTCACCTGCTCCTTTGCTGTCAGTGAAGTGG
GTGGTCATGTTTTTCTGGGGGGCTACCAATACTTCCTGTGAGTCTACTATGTATCCGAAAGTGGTACAGGACCTCTGTGG
CTGGAGAATCCGGAGCCTGGCTTGCGGGAAGAGCAGCATCATCGTGGCCGCAGACGAGAGCACCATCAGCTGGGGCCCAT
CGCCGACCTTCGGGGAACTGGGCTACGGGGACCACAAGCCCAAATCTTCCACTGCAGCCCAAGAGGTGAAGACTCTGGAT
GGCATCTTCTCAGAGCAGGTCGCCATGGGCTACTCACACTCCTTGGTGATAGCAAGAGATGAAAGCGAGACTGAGAAAGA
GAAGATCAAGAAACTGCCAGAGTACAACCCCTGAACCCTC

Alignment

ORF - retro_ogar_2967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPRKKAAAAAWEEPSSGNGTARAGPRKRGGLAGRKRERPERCSSSSGGGSSGDEDGLELDGAPGGGKRAA
          MPRK.AAAAAWEEPSSGNGTARAGPRKRGGLAGRKRERPERCSSSS.GG..GDEDGLELDGAPGGGK...
Retrocopy MPRKEAAAAAWEEPSSGNGTARAGPRKRGGLAGRKRERPERCSSSSSGG--GDEDGLELDGAPGGGKCXX

Parental  RPAAAGKAGGAAVVITEPEHTKERVKLEGSKCKGQLLIFGATNWDLIGRKEVPKQQAAYRNLGQNLWGPH
          .............V.TEPEHTKERVKLEGSKCKGQLLI.GATNWDLIG.KEVPKQQAAYRNLGQNLWGPH
Retrocopy XXXXXXXXXXXXXVVTEPEHTKERVKLEGSKCKGQLLILGATNWDLIGQKEVPKQQAAYRNLGQNLWGPH

Parental  RYGCLAGVRVRTVVSGSCAAHSLLITTEGKLWSWGRNEKGQLGHGDTKRVEAPRLIEGLSHEVIVLAACG
          RYGCLAGVRVRTVVSGSCAAHSLLITTEGKLWSWGRNEKGQLGHGDTKRVEAPRLIEGLSHEVIVLAACG
Retrocopy RYGCLAGVRVRTVVSGSCAAHSLLITTEGKLWSWGRNEKGQLGHGDTKRVEAPRLIEGLSHEVIVLAACG

Parental  RNHTLALTETGSVFAFGENKMGQLGLGNQTDAVPSPAQIMYNGQPITKMACGAEFSMIMDCKGNLYSFGC
          RNHTLALTETGSVFAFG.NKMGQLGLGNQTDAVPSPAQI.Y.GQPITKMACGAEFSMIMDCKGNLYSFGC
Retrocopy RNHTLALTETGSVFAFG*NKMGQLGLGNQTDAVPSPAQIVYSGQPITKMACGAEFSMIMDCKGNLYSFGC

Parental  PEYGQLGHNS-DGKFIARAQRIEYDCELVPRRVAIFIEKTKDGQILPVPNVVVRDVACGANHTLVLDSQK
          PEYGQLGHNS.DGKFIA.AQRIEYDCELVPRRVAIFIEKTKDGQILPVPNVVVRD.ACGANHTLVLDSQK
Retrocopy PEYGQLGHNS<DGKFIAWAQRIEYDCELVPRRVAIFIEKTKDGQILPVPNVVVRDMACGANHTLVLDSQK

Parental  RVFSWGFGGYGRLGHAEQKDEMVPRLVKLFDFPGRGASQIYAGYTCSFAVSEVGG-LFFWGATNTSREST
          RVFSWGF.GYGRLGHAEQKDEMVPRLVKLFDFP.RGASQIYAG.TCSFAVSEVGG..FFWGATNTS.EST
Retrocopy RVFSWGFSGYGRLGHAEQKDEMVPRLVKLFDFPDRGASQIYAGFTCSFAVSEVGG>MFFWGATNTSCEST

Parental  MYPKAVQDLCGWRIRSLACGKSSIIVAADESTISWGPSPTFGELGYGDHKPKSSTAAQEVKTLDGIFSEQ
          MYPK.VQDLCGWRIRSLACGKSSIIVAADESTISWGPSPTFGELGYGDHKPKSSTAAQEVKTLDGIFSEQ
Retrocopy MYPKVVQDLCGWRIRSLACGKSSIIVAADESTISWGPSPTFGELGYGDHKPKSSTAAQEVKTLDGIFSEQ

Parental  VAMGYSHSLVIARDESETEKEKIKKLPEYNPRTL
          VAMGYSHSLVIARDESETEKEKIKKLPEYNP.TL
Retrocopy VAMGYSHSLVIARDESETEKEKIKKLPEYNP*TL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2967 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 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	ENSOGAG00000007469	1 retrocopy	retro_ogar_704,
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,