RetrogeneDB ID: retro_ogar_1012

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873533.1:9902857..9903546(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PM20D2
• Ensembl ID: ENSOGAG00000005200
• Aliases: None
• Description: peptidase M20 domain containing 2 [Source:HGNC Symbol;Acc:21408]

Sequence

>retro_ogar_1012
GTGACTGTGAAATACTATGGAAAAGCATCTCATGTTGCTGCTTATCTCTGGGAGGGAGTAAATGTGTTAGATGCTGCCAT
CCTGGCCTACAGCAATCTATCCATGTTAAGACAGCAGATGAAACCCACCTGAAGAGTTCATGGTGTAATAAAAAATGGTG
GTACAAAACCCAATATCATTCCCTCTTATTTTGAATTAATCTATTACTTCCATGCCCCCTCAATGAAAGAGCTTCAAGTT
TTGAACAAAAAGGCAGAAGATTGCTTCAGAGCTGCAGCTTTGGCCACAGGGTGCACAGTGGAAATTAAAGGTGGAGCATA
TGATTATTATAATGTCCTTCCCAATAAGAGCCTGTGGAAAGCTTATATGGAAAATGGAGAAAAGCTGGGAATATAATTCA
TTTCAGAAGATACAATGTTGAGTGGCCCTTCAGGATCTACTGATTTTGGAAATGTGACTTTGTGTTTCCTGGAATTCATC
CGTATTTTTACATTGGGTCTAAAGCCTTGAATCATACTGAGCAATACACTGAGGCTGCAGGATCTCAAAAAGCTCAGTTC
TACACTTTGCATACAGCCAAAGCTCTTGCAATGACTACACTGGATGTTATTTTTAAACCAGAGTTGCTGGAAAAAATCAG
GGAGGACTTTAAATTGAAACTTCAAAAACAATTTTTAAATACAGTAGAA

Alignment

ORF - retro_ogar_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.05 %
• Parental protein coverage: 52.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTVKYYGKASHAAAYPWEGVNALDAAVLAYTNLSTLRQQMKPTWRVHGVIKNGGVKPNIIPSYSELIYYF
          VTVKYYGKASH.AAY.WEGVN.LDAA.LAY.NLS.LRQQMKPT.RVHGVIKNGG.KPNIIPSY.ELIYYF
Retrocopy VTVKYYGKASHVAAYLWEGVNVLDAAILAYSNLSMLRQQMKPT*RVHGVIKNGGTKPNIIPSYFELIYYF

Parental  RAPSMKELQVLTKKAEDCFRAAALATGCTVEIKGGAHDYYNVLPNKSLWKAYMENGEKLGIEFISEDTML
          .APSMKELQVL.KKAEDCFRAAALATGCTVEIKGGA.DYYNVLPNKSLWKAYMENGEKLGI.FISEDTML
Retrocopy HAPSMKELQVLNKKAEDCFRAAALATGCTVEIKGGAYDYYNVLPNKSLWKAYMENGEKLGI*FISEDTML

Parental  SGPSGSTDFGNVT-FVVPGIHPYFYIGSKALNHTEQYAEAAGXXXXXXXXXXXXXXXXXXXLDVIFKPEL
          SGPSGSTDFGNVT.FV.PGIHPYFYIGSKALNHTEQY.EAAG...................LDVIFKPEL
Retrocopy SGPSGSTDFGNVT<FVFPGIHPYFYIGSKALNHTEQYTEAAGSQKAQFYTLHTAKALAMTTLDVIFKPEL

Parental  LEKIREDFKLKLQEEQFLNTVE
          LEKIREDFKLKLQ..QFLNTVE
Retrocopy LEKIREDFKLKLQ-KQFLNTVE

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_1012 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
Cavia porcellus	ENSCPOG00000010921	1 retrocopy	retro_cpor_790,
Otolemur garnettii	ENSOGAG00000005200	1 retrocopy	retro_ogar_1012 ,