RetrogeneDB ID: retro_ogar_1720

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873562.1:12098878..12099264(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028802
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TNFRSF12A
• Ensembl ID: ENSOGAG00000008584
• Aliases: None
• Description: tumor necrosis factor receptor superfamily, member 12A [Source:HGNC Symbol;Acc:18152]

Sequence

>retro_ogar_1720
ATGGCTTGCGGCTTGCTGCGACCGATGTTGCCGATCCTCTTGCTGGGGCTAGGGCTGGCACAGCTGCGCGCAGCGTCCGA
GGAGCAAGCGCCAGGCACCGCCCGGTGCTCTAGCGGCAGCTCTTGGAGCGCGGACCTAGACAAGTGCATGGATTGTGCGT
CGTGCCAGGCGCGACCACACAGCGATTCTGCCTGGGCTGCCCTGCCGCACCTCCTGCCCCCTTCCAGCTACTTTGGCCCA
TCCTAGGGGGCGCCCTGAGCCTGACCCTGGTGCTGGGCCTGCTTTCTGGCTTCCTGGTCTGGAGACGGTGCCGCAGGAGA
GAGAAGTTCACCACCCCCATAGGGGAGATCAGAGGAGAGGGCTGTCCAGCCGTGGCCTTGATCCAG

Alignment

ORF - retro_ogar_1720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MACGSLRPMLRILVLGLGLALLRAASGEQAPGTAPCSSGSSWSADLDKCMDCASCPARPHSD-FCLGCAA
          MACG.LRPML.IL.LGLGLA.LRAAS.EQAPGTA.CSSGSSWSADLDKCMDCASC.ARPHSD.FCLGC.A
Retrocopy MACGLLRPMLPILLLGLGLAQLRAASEEQAPGTARCSSGSSWSADLDKCMDCASCQARPHSD<FCLGCPA

Parental  APPAPFRLLWPILGGALSLALVLGLLSGFLVWRRCRRREKFTTPIEETGGEGCPAVALIQ
          APPAPF.LLWPILGGALSL.LVLGLLSGFLVWRRCRRREKFTTPI.E..GEGCPAVALIQ
Retrocopy APPAPFQLLWPILGGALSLTLVLGLLSGFLVWRRCRRREKFTTPIGEIRGEGCPAVALIQ

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_1720 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000026197	1 retrocopy	retro_fcat_1365,
Mustela putorius furo	ENSMPUG00000015243	1 retrocopy	retro_mputfur_745,
Otolemur garnettii	ENSOGAG00000008584	1 retrocopy	retro_ogar_1720 ,