RetrogeneDB ID: retro_ogar_1034

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873534.1:18679562..18680892(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG4C
• Ensembl ID: ENSOGAG00000004020
• Aliases: None
• Description: autophagy related 4C, cysteine peptidase [Source:HGNC Symbol;Acc:16040]

Sequence

>retro_ogar_1034
ATGGAGGCCACAGGAACAGATGAAGTTGATAAGTTAAAAACTAAATTTGTATCTGCTTGGAACAACATGAAATATAGTTG
GGTATTAAAAACAAAGATGTATTTTAGTAGAAATTCCCTTGTATTACTACTTGCAAAATGTTACTATTTTAAATATGAAG
ATGAAAGTGGAATGTTACCTGCAAGATCAAGATGTACAATAGAAGATCATGTAATTGCGGGAAATATAAAAGAATTTCAT
AAAGATTTTATTTCTAGAATATGGCTGACTTACAGAGAAGAATTTCCTCAAATAGAAGGCTCAGCTTTGACAACAGACTG
TGGTTGGGGTGTACATTGAGAATTGGCCAGATTATGTTGGCTCAAGGACTCATACTACACTTTTTTGGTAGAGCTTGGAC
CTGGCCTGGTGCTTTGAATATCGAAAATTCAGACACTGAATCATGGACTTCCCACATTGTAAGAAAAATTTACTGAATCA
TTTGAAGCATTGCTTTCAGGGGAAAGTGAACTCAAAACCCCAAAAATTTCTCTGAAGGAAACAATGAGGAAATATTCTGA
TGATTATGAAATGTGAAATGAAATTTATCACAGGAAAATCATCTCTTGGTTTGGTGATTCCCCCTTGGCTTTCTTTGGCT
TGCATCAACTAATAGAGTATGGAAAGAAATCTGGGAAAAAAGCGGGAGATTGGTATGGACCAGCTGTGGGTTGCGCACAT
TTGAAGAAAAGCAGTTGAAGAAGCAAAACATTCTGATTTACAAAGAGTAACTATTTATGTTGCACAAGATTGTACAGTTT
ACAATTCTGATGTAATTGATAAGCAGAGCACTTCCAGGACCTCTGATAATGCAGAAGACAAAGCTGTTATTACTCTGGTT
CTTGTTAGATTTGGTGGAGAAAGAACCAACACTGACTACTTAGAGTTTGTAAAGGGTATTTTAAGCCTTGAATATTGTGT
GGATATTATTGGGGGCAAACCTAAACAGTCATATTACTTTGCAGGATTTCAAGATGACAGTCTGATTTACATGGATCCTC
ATTACTGCCAACCTTTTGTAGATGTCAGCGTAAAGAATCTCCCACTTGAGATATTCCACTGCCCTTCTCCCAAAAAGATG
TCATTTTGAAAAATGGATCCTAGCTGTACAATAAGATTATATTGTCGAAACGTTCAGGACTTTGAATGAGTACCTGAAGA
AATCACCAAGAAGCTGAAAATTTCTTCCAAGGAGAAATATCCCTTATTTACTTTTGTAAATGGTCATTCCAGAGACTATG
ATTTTACATCTACTACAACCGATGAAGACCTTTTCACAGTGGATGAAAAG

Alignment

ORF - retro_ogar_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.0 %
• Parental protein coverage: 96.94 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEATGTDEVDKLKTKFVSAWNNMKYSWVLKTKTYFSRNSPVLLLGKCYHFKYEDENEMLSARSGCTIEDH
          MEATGTDEVDKLKTKFVSAWNNMKYSWVLKTK.YFSRNS.VLLL.KCY.FKYEDE..ML.ARS.CTIEDH
Retrocopy MEATGTDEVDKLKTKFVSAWNNMKYSWVLKTKMYFSRNSLVLLLAKCYYFKYEDESGMLPARSRCTIEDH

Parental  VIAGNVEEFRKDFISRIWLTYREEFPQIEGSALTTDCGWG-CTLRTGQMLLAQGLILHFLGRAWTWPGAL
          VIAGN..EF.KDFISRIWLTYREEFPQIEGSALTTDCGWG.CTLR.GQ..LAQGLILHF.GRAWTWPGAL
Retrocopy VIAGNIKEFHKDFISRIWLTYREEFPQIEGSALTTDCGWG<CTLRIGQIMLAQGLILHFFGRAWTWPGAL

Parental  NIENSDSESWTSHTVKK-FTASFEASLSGERELKTPTISLKETMRKYSDYHETRNEIYHRKIVSWFGDSP
          NIENSD.ESWTSH.V.K.FT.SFEA.LSGE.ELKTP.ISLKETMRKYSD..E..NEIYHRKI.SWFGDSP
Retrocopy NIENSDTESWTSHIVRK>FTESFEALLSGESELKTPKISLKETMRKYSDDYEM*NEIYHRKIISWFGDSP

Parental  LAFFGLHQLIEYGKKSGKKAGDWYGPAV-VAHILRKAVEEAKHPDLQGITIYVAQDCTVYNSDVIDTQSA
          LAFFGLHQLIEYGKKSGKKAGDWYGPAV.VAHI.RKAVEEAKH.DLQ..TIYVAQDCTVYNSDVID.QS.
Retrocopy LAFFGLHQLIEYGKKSGKKAGDWYGPAV>VAHI*RKAVEEAKHSDLQRVTIYVAQDCTVYNSDVIDKQST

Parental  SRTSEGAEDKAVIILVPVRLGGERTNPDYLEFVKGILSLEYCVGIIGGKPKQSYYFAGFQDDSLIYMDPH
          SRTS..AEDKAVI.LV.VR.GGERTN.DYLEFVKGILSLEYCV.IIGGKPKQSYYFAGFQDDSLIYMDPH
Retrocopy SRTSDNAEDKAVITLVLVRFGGERTNTDYLEFVKGILSLEYCVDIIGGKPKQSYYFAGFQDDSLIYMDPH

Parental  YCQPFVDVSVKDFPLETFHCPSPKKMSFRKMDPSCTIGFYCRNVQDFERTSEEITKMLRISAKEKYPLFT
          YCQPFVDVSVK..PLE.FHCPSPKKMSF.KMDPSCTI..YCRNVQDFE...EEITK.L.IS.KEKYPLFT
Retrocopy YCQPFVDVSVKNLPLEIFHCPSPKKMSF*KMDPSCTIRLYCRNVQDFE*VPEEITKKLKISSKEKYPLFT

Parental  FVNGHSRDYDFTSTTTNEDLFSEDEK
          FVNGHSRDYDFTSTTT.EDLF..DEK
Retrocopy FVNGHSRDYDFTSTTTDEDLFTVDEK

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_1034 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000004020	1 retrocopy	retro_ogar_1034 ,
Procavia capensis	ENSPCAG00000003461	1 retrocopy	retro_pcap_299,