RetrogeneDB ID: retro_ogar_1110

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873536.1:8128919..8130209(+)
• Located in intron of: ENSOGAG00000003713

Retrocopy information

• Ensembl ID: ENSOGAG00000027981
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP2M1
• Ensembl ID: ENSOGAG00000012286
• Aliases: None
• Description: adaptor-related protein complex 2, mu 1 subunit [Source:HGNC Symbol;Acc:564]

Sequence

>retro_ogar_1110
ATGGTTGGAGACTTATTCATCTATAATCACAAGGGGGAGGTACTTATCTCCCGGGTCTACCGAGATGACATCGGGAGAAA
TGCAGTGGATGCCTTTCGGGTCAACGTTATCCACGCCCGGCAGCAGGTGCGCAGCCCTGTCACCAACATGGCTTGCACCA
GCTTTTTTCATGTTAAGCGGTCCAACATCTGGCTGGCAGCAGTCACCAAGCAAAATGTCAACGCTGCCATGGTCTTCAAA
TTCCTCTATAAGATGTGTGACGTAATGGCTGCCTACTTTGGCAAGATCAGCGAGGAAAACATCAAGAATAATTTTGTGCT
CATATATGAGCTGCTGGATGAGATCCTGGACTTTGGCTACCCACAGAACTCTGAGACAGGTGCGCTGAAGACCTTCATCA
CACAGCAGGGCATCAAGAGTCAGCATCAGACAAAAGAAGAGCAATCTCAGATCACCAGCCAGGTGACTGGGCAGATTGGC
TGGCGGCGAGAGGGCATCAAGTACCATAGGAATGAGCTCTTCCTGGATGTGCTGGAAAGTGTGAACCTGCTCATGTCCCC
ACAGGGGCAGGTGCTGAGTGCCCATGTGTCAGGCTGGGTGGTGATGAAGAGCTACCTGAGTGGCATGCCTGAGTGCAAGT
TTGGGATGAATGACAGGATTGTCATTGAAAAGCAGGGCAAAGGCACAGCAGATGAAATGAGCAAGAGTGGGAAACAATCA
ATTGCCATTGATGACTGCACTTCTACCAGTGTGTGCGTCTCAGCAAGTGTGACTCTAGCATCAGCTTCATCCCACCAGAT
GGAGAATTTGAACTCATGAGGTATCGCACCACCAAGGACATCATGCTTCCTTTCCAGGTAATCCTGCACTAGCAGGAGTG
GGACGCACCAGATTAGAGGTCAAAGTGGTCATCAAGTCCAACTTCAAGCCCTCCCTGCTGGCTCAGAAGATTGAGGTGAG
AATCCCAACCCCACTGAACACAAACGGGGAGCAGGTGATCTGCATGAAGGGGAAGGCCAAGTACAAGGCCAGCGAGAACG
CCTTGTGTGGAAGATCAAGCACGTGGCGGGCATGAAGGAATCGCAGATCAGTGCAGAGATTGAGCTTCTTCCCACCAATG
ACAAGAAGAAATGGGCTCGGCCCCCCATTTCCATGAACTTTGAGGTGCCATTCGCACCCTCTGGCTTCAAGGTGCACTAC
TTGAAGGTGTTTGAACTGAAACTGAACTACAGCGACCATGATGTCATCAAATGGGTGTGCTACATTGGTTGCAGTGGCAT
TTATGAAACT

Alignment

ORF - retro_ogar_1110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.01 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTK
          M.G.LFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTN.A.TSFFHVKRSNIWLAAVTK
Retrocopy MVGDLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNMACTSFFHVKRSNIWLAAVTK

Parental  QNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKS
          QNVNAAMVF.FLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKS
Retrocopy QNVNAAMVFKFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKS

Parental  QHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQAPGQVLSAHVSGRVVMKSYLSG
          QHQTKEEQSQITSQVTGQIGWRREGIKY.RNELFLDVLESVNLLMSPQ..GQVLSAHVSG.VVMKSYLSG
Retrocopy QHQTKEEQSQITSQVTGQIGWRREGIKYHRNELFLDVLESVNLLMSPQ--GQVLSAHVSGWVVMKSYLSG

Parental  MPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCT-FHQCVRLSKFDSERSISFIPPDGEFELMRY
          MPECKFGMND.IVIEKQGKGTADE.SKSGKQSIAIDDCT.F.QCVRLSK.DS..SISFIPPDGEFELMRY
Retrocopy MPECKFGMNDRIVIEKQGKGTADEMSKSGKQSIAIDDCT<FYQCVRLSKCDS--SISFIPPDGEFELMRY

Parental  RTTKDIILPFRVI-PLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKA
          RTTKDI.LPF.VI.P....VGRT.LEVKVVIKSNFKPSLLAQKIEVRIPTPLNT.G.QVICMKGKAKYKA
Retrocopy RTTKDIMLPFQVI<PALAGVGRTRLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTNGEQVICMKGKAKYKA

Parental  SENA-IVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSD
          SENA..VWKIK..AGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSG.KV.YLKVFE.KLNYSD
Retrocopy SENA<LVWKIKHVAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGFKVHYLKVFELKLNYSD

Parental  HDVIKWVRYIGRSGIYET
          HDVIKWV.YIG.SGIYET
Retrocopy HDVIKWVCYIGCSGIYET

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_1110 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020106	1 retrocopy	retro_btau_1156,
Canis familiaris	ENSCAFG00000012257	2 retrocopies	retro_cfam_1923, retro_cfam_2028,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Mus musculus	ENSMUSG00000022841	2 retrocopies	retro_mmus_1873, retro_mmus_1914,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98,
Otolemur garnettii	ENSOGAG00000012286	1 retrocopy	retro_ogar_1110 ,
Rattus norvegicus	ENSRNOG00000001709	1 retrocopy	retro_rnor_2342,
Tursiops truncatus	ENSTTRG00000008493	1 retrocopy	retro_ttru_522,