RetrogeneDB ID: retro_ogar_2492

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873628.1:4447932..4448811(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000025898
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A6
• Ensembl ID: ENSOGAG00000000963
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6 [Source:HGNC Symbol;Acc:10992]

Sequence

>retro_ogar_2492
AGCATGACAGATGCCTTTGTGTCCTTCATCAAGGACTTCCCGGCAGGTGGAGTGGCCATGGCCATTTCTAAGACCACAGT
AGCACCCATCCAGTCAGTCAAGCTGCTGCTGCAGGTACAACATGCCAGCAAGCAAATCACTGCGCATAAGCAATACAAAG
GCATTATTAGACTGCGCGGTCCATATCCCCAAAGAGCAGGGAGTCCTGTCCTTCTGGCGTGGTAACCTGGCCAATGTCAT
CTGTTACTTCCCCACTCAGGCTCTCAACTTTGCCTTCAAAGATAAATACAAGCAGATCTTCCTGGGTGGTGTGGACAAGA
GGACCCAGTTTTGGTGCTACTTTGCAGGGAATCTGGCATCAGGTGGTGCCGCTGGGGCCACATCCTTGTGTTTTGTGTAC
CCTCTTGATTTTGCTCGTACCCGTCTAGTGGCTGATGAGGGTAAAGCTGGAGTGGAAAGAGAATTCAAAGGCCTTGGCGA
CTGCCTGGTTAAGATTTACAAATCTGATGGGCTTAGGGGCCTGCATGAAGGCTTTAACGTGTCTGTCCAGGGTATTATCA
TCTACCGAGCTGCCTACTTCAGTATCTGTGACACTCCAAAGGGAATGCTTCCAGATCCCAGGAATACTCACATCATCATC
AGCTGGATGATTGCAACTGTCACTGTCACTGGCTTCCTATCCTTTGGCACTGTTTGCGTGGCATGATGATGCAGTCAGGG
CGCAATGGAATTGACATCATGTACACCGGCAAGGTTGACTGCTGGAGAAAGATCCTTCCTGATAAAGGAGGCAAAGCTTT
AATCAAGCGTGCATGGTCCACTGTTCTCAGAGGCATAGGTGGTGCTTGTGTGCTTGTCTTATACGATGAAATCAAGAAG

Alignment

ORF - retro_ogar_2492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 92.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TMTEQAISFAKDFLAGGIAAAISKTAVAPIERVKLLLQVQHASKQIAADKQYKGIV-DCVVRIPREQGVL
          .MT....SF.KDF.AGG.A.AISKT.VAPI..VKLLLQVQHASKQI.A.KQYKGI..DC.V.IP.EQGVL
Retrocopy SMTDAFVSFIKDFPAGGVAMAISKTTVAPIQSVKLLLQVQHASKQITAHKQYKGII>DCAVHIPKEQGVL

Parental  SFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKHTQFWRYFAGNLASGGAAGATSLCFVYPLDFAR
          SFWRGNLANVI.YFPTQALNFAFKDKYKQIFLGGVDK.TQFW.YFAGNLASGGAAGATSLCFVYPLDFAR
Retrocopy SFWRGNLANVICYFPTQALNFAFKDKYKQIFLGGVDKRTQFWCYFAGNLASGGAAGATSLCFVYPLDFAR

Parental  TRLAADVGKSGAEREFKGLGDCLVKITKSDGVRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNT
          TRL.AD.GK.G.EREFKGLGDCLVKI.KSDG.RGL..GFNVSVQGIIIYRAAYF...DT.KGMLPDP.NT
Retrocopy TRLVADEGKAGVEREFKGLGDCLVKIYKSDGLRGLHEGFNVSVQGIIIYRAAYFSICDTPKGMLPDPRNT

Parental  HIVVSWMIAQTVTAVAGVVSYPFDTV-RRRMMMQSGRKGADIMYKGTVDCWRKIFRDEGGKAFFKGAWSN
          HI..SWMIA.TVT.V.G..S..F.TV..R.MMMQSGR.G.DIMY.G.VDCWRKI..D.GGKA..K.AWS.
Retrocopy HIIISWMIA-TVT-VTGFLS--FGTV<LRGMMMQSGRNGIDIMYTGKVDCWRKILPDKGGKALIKRAWST

Parental  VLRGMGGAFVLVLYDELKK
          VLRG.GGA.VLVLYDE.KK
Retrocopy VLRGIGGACVLVLYDEIKK

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_2492 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005609	1 retrocopy	retro_amel_255,
Homo sapiens	ENSG00000169100	5 retrocopies	retro_hsap_1207, retro_hsap_150, retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla	ENSGGOG00000023004	2 retrocopies	retro_ggor_239, retro_ggor_2785,
Loxodonta africana	ENSLAFG00000001584	1 retrocopy	retro_lafr_713,
Microcebus murinus	ENSMICG00000006136	2 retrocopies	retro_mmur_1021, retro_mmur_922,
Macaca mulatta	ENSMMUG00000006899	1 retrocopy	retro_mmul_1182,
Nomascus leucogenys	ENSNLEG00000000389	1 retrocopy	retro_nleu_895,
Otolemur garnettii	ENSOGAG00000000963	2 retrocopies	retro_ogar_2492 , retro_ogar_2499,
Otolemur garnettii	ENSOGAG00000010008	7 retrocopies	retro_ogar_1131, retro_ogar_1275, retro_ogar_1669, retro_ogar_2161, retro_ogar_2408, retro_ogar_2450, retro_ogar_2474,