RetrogeneDB ID: retro_ogar_1212

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873539.1:17228168..17228516(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSOGAG00000004388
• Aliases: None
• Description: GABA(A) receptor-associated protein [Source:HGNC Symbol;Acc:4067]

Sequence

>retro_ogar_1212
ATGAAGTTTGTGTACAAAGAGGAGCATCCGTTTGAGAAGTGCCACTCTGAGGGCAAGAAGATCCAAAAGAAATACCCGGA
CCGGGTCCCGGTGATAGTAGAAAAGGCACCCAAAGCTCGGATAGGAGACCTGGACAAAAAGAAATACCTGGTGCCTTCTG
ATCTCACAGTTGGTCAATTCTACTTCTTGATCCGGAAGCGAATTCATCTCTGAGCTGAGGATGCCTTGTTCTTCTTTGTC
AACAATGTCATTCCACCTACCAGTGCCACTATGGGTCAGCTATACCAGGAACACCACGAAGATTTCTTTCTATACATTGC
CTACAGTGATGAAAGTGTCTACAGTCTG

Alignment

ORF - retro_ogar_1212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
          MKFVYKEEHPFEK..SEG.KI.KKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
Retrocopy MKFVYKEEHPFEKCHSEGKKIQKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL

Parental  RAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
          .AEDALFFFVNNVIPPTSATMGQLYQEHH.EDFFLYIAYSDESVY.L
Retrocopy *AEDALFFFVNNVIPPTSATMGQLYQEHH-EDFFLYIAYSDESVYSL

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_1212 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Echinops telfairi	ENSETEG00000004652	7 retrocopies	retro_etel_1020, retro_etel_1078, retro_etel_1562, retro_etel_2068, retro_etel_493, retro_etel_666, retro_etel_976,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Mustela putorius furo	ENSMPUG00000010473	2 retrocopies	retro_mputfur_1290, retro_mputfur_258,
Otolemur garnettii	ENSOGAG00000004256	3 retrocopies	retro_ogar_1468, retro_ogar_2885, retro_ogar_2892,
Otolemur garnettii	ENSOGAG00000004388	2 retrocopies	retro_ogar_1212 , retro_ogar_1224,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,