RetrogeneDB ID: retro_ogar_3417

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873824.1:94173..96469(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028065
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MATR3
• Ensembl ID: ENSOGAG00000010607
• Aliases: None
• Description: matrin 3 [Source:HGNC Symbol;Acc:6912]

Sequence

>retro_ogar_3417
CTTCTTCCCATATTTAACATTGGAAGTAGAGGTTCACTCCCTTTATCTTCTCAACACCGTGGAGATGTAGACCAAGCCAG
TAACATTTTGGCCAGCTTTGGTCTGTCTGCTAGAGACTTAGATGAACTGAGTTGTTATCCAGAGGACAAGATTACTCCTG
AGAATTTGCCCCAGATCCTTCTACAGCGTAAAAGGAGGAGAACTGAAGAAGGCCCTACATTGAGTTATGGTAGAGATGGC
AGATCTGCTACATGGAGCCACCATACAGAGTACCTAGGGATGACTGGGAAGAAAAAAGTCACTTTAGAAGAGATAGTTTT
GATGATCATGGTCCTAGTCTCAACCCAGTGCTTGATTATGACCATGGAAGTCATTCTCAAGAATCTGGTTATTATGACAG
AATGGATTATGAAGATGACAGATTAAGAGATGGAGAAAGGTTTAAGGATGATTCTTTTTTTGGTGAGACCTCGCATAACT
ATCATAAATTTGACAGTGAGTATGAGAGAATGGGACATGGTCCTGGCCCCTTACAAGAGAGATCTCTCTTTGAGAAAAAG
AGGGGTGCTCCTCCAAGTAGCAATATTGAAGACTTCCATGGACTCTTACCGAAGGGTTATCCCCATCTGTGCTCTATATG
TGATTTGCCAGTTCATTCTAATAAGGAGTGGAGTCAACATATCAATGGAGCAATTCACAGTCGTCGATGCCAGCTTCTTC
TTGAAATCTATCCAGAATAGAATCCTGACAATGATACAGGACACACAATGGGTGATCCCTTCATGTTGCAGCAGTCCACA
AACCCAGGGCCAGGAATTCTGGGACCTCCACCTCCCTCATTCCATCTTGGGCGACCAGCAGTTGGACCAAGAGGAAATCT
GGTTACTGGAAATGGGAACCTGCAAGGACCTAGACACATGCAGAAAGGCAGAGTAGAAACTAGCCGAGTTGTTCACATCA
TGGATTTTCAATGAGGGAAAAACTTGAGATACCAACTATTACAGCTTGTGGAACCATCTGAAGTCATTTCAAATCATCTG
ATTCTAAATAAAATTAATGAGGCTTTTATTGAAATGGCAACTACAGAGGATGCTCAGGCTGCAGTGGATTATTATACAAC
CACGCCAGCATTAGTGTTTAGCAAGCCAGTGAGAGTCCATTTATCCCAGAAGTATAAAAGAATAAAGAAGCCCAAGGGGA
AGCCAGATCAGAAGTTTGATCAAAAGCAAGAGCTTGGACATGTAATACATCTTAGCAATTTGCCCCATTCTGGCTATTCT
GATAGTGCTATTCTAAAGCTTGCTGAGCTTTATGGAAAAATAAAAAATTATATATTGATGAGGATGAAGAGTCAGGCCTT
CATTGAGATGGAGACAAGAGAAGATGCAATGGCAATGGTTGACCATTGTTTGAAAAAAGCCCTTTGCTTTCAGGGGAGAG
ATGTATAAAGGTTGACCTTTCTGAAAAATACAAAAAACTGGTACTGAGGATTCCTAACACAGGCATTGACTTACTGAAAA
AAGATAAATCCCGAAAAAGGTCTTATTCTCCAGATGGCAAAGAATCTCTAAGTGATAAGAAATCTAAAACTGATGGTTCC
AGAAGACTTAAAGTACAACTGAAGGTAAAGAACAAGAAGAAAAGTCAGGTGAAGATGGTGACAAAGATACAAAGGATGAC
CAGACAGAACAGGAACCCAGTATGCTTCTCGAATCTGAAGATGAGCTGGTTGTAGATGAAGAAGAAGCAGCTGCATTATT
AGAAAGTGGCAGTTCAGTGGGAGATGAGACTGATCTTGCTAATTTAGGTGATGTGGCTTCTGATGGGAAAAAAGGAGGCT
TCAGATAAAGCTGTGAAAAAAGATGCAACTGCTTCAGCAGCAGCAAAGAAAAAGCTTAAAAAGGTGGACAAGATCAAGGA
ACTTGATCAAGAAAATGAAGCAGCGTTGGAAAATGGAATTAAAAATGAGGAAAATACAGAACCAGGTGCAGAATCTGCTG
AGAATGCTGATAATCCCAACAAAGATACAAGTGAAAATGCAGATGGACAAAGTGATGAAAACAAGGAGGACTATACAATC
CCAGATGAGTATAGACTTGGACCACATCAGCCCAATGTTCTTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTA
CTATAAGCTGTGTTCGCTCTGTTATACAAATGAAGAAGTTGCAAAGAAAACTCATTGCAGCAGCCTTCCTCATTATCAGA
AATTAAAGAAATTTCTGAATAAATTGGCAGAGGAATGCAGACAAAAGAAGGAAACA

Alignment

ORF - retro_ogar_3417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.25 %
• Parental protein coverage: 90.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LQSIFNIGSRGPLPLSSQHRGDADQASNILASFGLSARDLDELSRYPEDKITPENLPQILLQLKRRRTEE
          L..IFNIGSRG.LPLSSQHRGD.DQASNILASFGLSARDLDELS.YPEDKITPENLPQILLQ.KRRRTEE
Retrocopy LLPIFNIGSRGSLPLSSQHRGDVDQASNILASFGLSARDLDELSCYPEDKITPENLPQILLQRKRRRTEE

Parental  GPTLSYGRDGRSAT-REPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQESGYYDRMDYED
          GPTLSYGRDGRSAT..EPPYRVPRDDWEEK.HFRRDSFDD.GPSLNPVLDYDHGS.SQESGYYDRMDYED
Retrocopy GPTLSYGRDGRSAT<MEPPYRVPRDDWEEKSHFRRDSFDDHGPSLNPVLDYDHGSHSQESGYYDRMDYED

Parental  DRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPH
          DRLRDGER..DDSFFGETSHNYHKFDSEYERMG.GPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPH
Retrocopy DRLRDGERFKDDSFFGETSHNYHKFDSEYERMGHGPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPH

Parental  LCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTNPAPGILGPPPP
          LCSICDLPVHSNKEWSQHINGA.HSRRCQLLLEIYPE.NPDNDTGHTMGDPFMLQQSTNP.PGILGPPPP
Retrocopy LCSICDLPVHSNKEWSQHINGAIHSRRCQLLLEIYPE*NPDNDTGHTMGDPFMLQQSTNPGPGILGPPPP

Parental  SFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL
          SFHLG.PAVGPRGNL..GNGNLQGPRHMQKGRVETSRVVHIMDFQ.GKNLRYQLLQLVEP..VISNHLIL
Retrocopy SFHLGRPAVGPRGNLVTGNGNLQGPRHMQKGRVETSRVVHIMDFQ*GKNLRYQLLQLVEPSEVISNHLIL

Parental  NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIHLS
          NKINEAFIEMATTEDAQAAVDYYTTTPALVF.KPVRVHLSQKYKRIKKP.GKPDQKFDQKQELG.VIHLS
Retrocopy NKINEAFIEMATTEDAQAAVDYYTTTPALVFSKPVRVHLSQKYKRIKKPKGKPDQKFDQKQELGHVIHLS

Parental  NLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALW-FQG-RCVKVDLS
          NLPHSGYSDSA.LKLAE.YGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL..F.G.RC.KVDLS
Retrocopy NLPHSGYSDSAILKLAELYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALC>FRG>RCIKVDLS

Parental  EKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGS-QKTESTTEGKEQEEKSGEDGEKD
          EKYKKLVLRIPN.GIDLLKKDKSRKRSYSPDGKES.SDKKSKTDGS.QKT.STTEGKEQEEKSGEDG.KD
Retrocopy EKYKKLVLRIPNTGIDLLKKDKSRKRSYSPDGKESLSDKKSKTDGS<QKT*STTEGKEQEEKSGEDGDKD

Parental  TKDDQTEQEPNMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVASDGKK-EPSDKAVKKDASAS
          TKDDQTEQEP.MLLESEDEL.VDEEEAAALLESGSSVGDETDLANLGDVASDGKK.E.SDKAVKKDA.AS
Retrocopy TKDDQTEQEPSMLLESEDELVVDEEEAAALLESGSSVGDETDLANLGDVASDGKK>EASDKAVKKDATAS

Parental  AAAKKKLKKVDKIEELDQENEAALENGIKNEENTEPGAESAENADDPNKDTSENADGQSDENKEDYTIPD
          AAAKKKLKKVDKI.ELDQENEAALENGIKNEENTEPGAESAENAD.PNKDTSENADGQSDENKEDYTIPD
Retrocopy AAAKKKLKKVDKIKELDQENEAALENGIKNEENTEPGAESAENADNPNKDTSENADGQSDENKEDYTIPD

Parental  EYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKKFLNKLAEERRQKKET
          EYR.GP.QPNV.VGIDYVIPKTGFY.KLCSL.YTNEEVAK.THCSSLPHYQKLKKFLNKLAEE.RQKKET
Retrocopy EYRLGPHQPNVLVGIDYVIPKTGFYYKLCSLCYTNEEVAKKTHCSSLPHYQKLKKFLNKLAEECRQKKET

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_3417 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006888	1 retrocopy	retro_cjac_3950,
Homo sapiens	ENSG00000015479	1 retrocopy	retro_hsap_199,
Gorilla gorilla	ENSGGOG00000007308	2 retrocopies	retro_ggor_276, retro_ggor_421,
Nomascus leucogenys	ENSNLEG00000009093	1 retrocopy	retro_nleu_1849,
Oryctolagus cuniculus	ENSOCUG00000026311	1 retrocopy	retro_ocun_652,
Otolemur garnettii	ENSOGAG00000010607	1 retrocopy	retro_ogar_3417 ,
Pongo abelii	ENSPPYG00000015835	2 retrocopies	retro_pabe_1722, retro_pabe_438,
Pan troglodytes	ENSPTRG00000017294	1 retrocopy	retro_ptro_181,
Rattus norvegicus	ENSRNOG00000019875	2 retrocopies	retro_rnor_1124, retro_rnor_475,