RetrogeneDB ID: retro_ogar_1842

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873569.1:1452724..1453620(-)
• Located in intron of: ENSOGAG00000011137

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL2
• Ensembl ID: ENSOGAG00000034421
• Aliases: None
• Description: mitochondrial ribosomal protein L2 [Source:HGNC Symbol;Acc:14056]

Sequence

>retro_ogar_1842
ATGGCTCTGTGGGCATTGACCCGTGCTCTGGGCTCCCTGAGCCTGACACCCTGGCAATCGCTGCTCCCATCTCAAGTCTG
CTCCCTGCTGCCCAAGTGATGAACAATGCCTTTCTTCAACTGCCCTCAGCCTTGATGTTGCTCCCCTGTTGCACAGACCT
TGCTTCTGTGGCCCTTATTGCCAAGTTTGTGTCCTGGAGGAGTCCTACGAAGTACCATTAGACCAATGAGGAAGAGGAAG
TCTGGGGGCCAAGACTACACAGGCCGCGTCCGAGTGCATGGTATGGGCGGGGCCACAAGCAACTTTATGGCATGATTGAT
TTTCTGTGTTTCCAGCCTGAATAGGAGACCAAGCCTGGACCCTTCGAGGAGAAGGTTGTCAGAGTCTGCAGGTCAGCAGA
CATAGCTCTGGTTGCTGGGGGCAGCCAGAAATGCTGGATTGTTGCCATAGAAAACATGCAGGCTGGAGATGTAACCCTGA
ATTCTTACCACATAGGCCACATGACTGTTGCTGCCCGGAAAGAAGATGCACATCCTCTTGGGGCCCTGCCTATGGGGATC
CTTGTCAACAACGTGGAAAATGAGCCAGGTCAGGGGCCCAGTATATCTGAGCTACAGGGACATGTAGTGTGCTGCTTCAG
AAGGTAAATGAGACCCCCCATTATCCAGTCACCTTCTAAGAGGCAGATGCAGGAGCTGGAAACTTGCATAGCAATAGTCA
GCCAAGTAGCCAACGTTGATCATAACAAACAGGTCATAGGAAAGGCGGGTCACAACCGCTGGGTAGGCAAGAAGCCTAAC
AACGGGCTATGGCATTGCAAGGGGGGCTGGGCTGGCCGAAAGATTTGGCCACTGTCCCCTGTGAAGTGTTATGTGAAGTT
GCCCTCTGCTGTTGCC

Alignment

ORF - retro_ogar_1842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALWALTRALGSLNLAPQ-AVAAPVSSLLPAAQVMNNAFLQLPSALTLLPYRTVLTSVALKAKFVSWKSH
          MALWALTRALGSL.L.P..A.AAP.SSLLPAAQVMNNAFLQLPSAL.LLP..T.L.SVAL.AKFVSW.S.
Retrocopy MALWALTRALGSLSLTPW<AIAAPISSLLPAAQVMNNAFLQLPSALMLLPCCTDLASVALIAKFVSWRSP

Parental  TKYTIRPLKKRKSGGRDHTGRIRVHGIGGGHKQLYRMIDFLRFRPEQETKPEPFEERVITVRYDPCRSAD
          TKY..........G.R.H..R......G.GHKQLY.MIDFL.F.PE.ETKP.PFEE.V..V....CRSAD
Retrocopy TKYH*TNEEEEVWGPRLHRPRPSA-WYGRGHKQLYGMIDFLCFQPE*ETKPGPFEEKVVRV----CRSAD

Parental  IALVAGGSRKRWIVATENMQAGDVILNSNHIGRMAVAAQEGDAHPLGALPVGTLVNNVESEPGR-GAQYI
          IALVAGGS.K.WIVA.ENMQAGDV.LNS.HIG.M.VAA...DAHPLGALP.G.LVNNVE.EPG..GAQYI
Retrocopy IALVAGGSQKCWIVAIENMQAGDVTLNSYHIGHMTVAARKEDAHPLGALPMGILVNNVENEPGQ<GAQYI

Parental  RAAGTCGVLLRKVNGT-AIIQLPSKRQMQVLETCIATVGRVSNVDHDKRVIGKAGRNRWLGKRPNSGLWH
          .A.GTC.VLL.KVN.T..IIQ.PSKRQMQ.LETCIA.V..V.NVDH.K.VIGKAG.NRW.GK.PN.GLWH
Retrocopy *ATGTCSVLLQKVNET>PIIQSPSKRQMQELETCIAIVSQVANVDHNKQVIGKAGHNRWVGKKPNNGLWH

Parental  RKGGWAGRKIRPLPPMKSYVKLPSAAA
          .KGGWAGRKI.PL.P.K.YVKLPSA.A
Retrocopy CKGGWAGRKIWPLSPVKCYVKLPSAVA

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_1842 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005134	1 retrocopy	retro_acar_136,
Callithrix jacchus	ENSCJAG00000005116	1 retrocopy	retro_cjac_3318,
Homo sapiens	ENSG00000112651	1 retrocopy	retro_hsap_1039,
Gorilla gorilla	ENSGGOG00000010552	1 retrocopy	retro_ggor_820,
Macaca mulatta	ENSMMUG00000002450	1 retrocopy	retro_mmul_827,
Nomascus leucogenys	ENSNLEG00000004370	1 retrocopy	retro_nleu_912,
Otolemur garnettii	ENSOGAG00000034421	2 retrocopies	retro_ogar_1582, retro_ogar_1842 ,
Pongo abelii	ENSPPYG00000016630	1 retrocopy	retro_pabe_871,
Pan troglodytes	ENSPTRG00000018186	1 retrocopy	retro_ptro_709,
Rattus norvegicus	ENSRNOG00000018057	1 retrocopy	retro_rnor_555,