RetrogeneDB ID: retro_ogar_1580

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873553.1:8346980..8347806(+)
• Located in intron of: ENSOGAG00000009993

Retrocopy information

• Ensembl ID: ENSOGAG00000030077
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAT2A
• Ensembl ID: ENSOGAG00000026925
• Aliases: None
• Description: methionine adenosyltransferase II, alpha [Source:HGNC Symbol;Acc:6904]

Sequence

>retro_ogar_1580
GTTCACCTTGACCAGAATGAGGAAGGCATTGGTGTTGGAGACCAGGGTTTGATGTTTGGCTATGCCACTGATGAAACTGA
GGGAGTGTATACTTTTAACCATTGTCCTAACATACAAGCTCAAGGCCAAATTAGCAGAACTACTCCAGAAAAGCACTTTG
CCTTGGTTACGCCCAGATTCTAAAACTCAAGTGACTATGCAGTATATGCAGGATCAAGGTGCTGTGCTTCCCATCAGAGT
TCACACAATTGTTATATCTGTTCAGCATGATGAAAAAGTTTGTCTTGATGAGATGAGGGATGCTCTAAAGAAGAAAGTTA
TCAAAGCTGTTGTACCTGCAAAATATCTTGTTGAATATACAATCTACCATCTACAGCCAAGTGGCAGATTCACTGTTGGT
GGGCCTCAGGTTGATGCTGGTTTGACTGGCTGGAAAATCACTGTGGACACTTACAGAGGTTGTAGAGCTCATGGAGGAGG
TGCCTTTTCAGGAACGGATTATACCAAGGTGGATCGTTCAGCTGCTTATGCTGCTCGTTGGGTGGCAAAATCCCTTGTTA
AAGGAGGTCTGTGCAGGAGGGTTCTTGTTCAGGTCTCTTACACTTTTGGACTTTCTCATGTATTATCTATCTCCATTTTC
CATTATGGTACCTCTCAGAAGAGTGAGAGAGAGCTATTAGAGACTGTGAAGAAGAATTTTGATCTCCACCCTGAGGATCA
TTGTCAGGGATCTGGATCTGAAGAAGCCAATTTATCAAAGGACTGCAGCCTAGGGCCACTTTGGTAGGACAGCTTCCCGT
GGGAATTGCCCCAAAAGCTTAAATAT

Alignment

ORF - retro_ogar_1580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.25 %
• Parental protein coverage: 69.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VHLDRNEEDIGAGDQGLMFGYATDETE-ECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYM
          VHLD.NEE.IG.GDQGLMFGYATDETE.EC..LTIVL..KL.AKLAEL....TLPWLRPDSKTQVT.QYM
Retrocopy VHLDQNEEGIGVGDQGLMFGYATDETE>ECILLTIVLTYKLKAKLAELLQKSTLPWLRPDSKTQVTMQYM

Parental  QDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDA
          QD.GAVLPIRVHTIVISVQHDE.VCLDEMRDALK.KVIKAVVPAKYL.E.TIYHLQPSGRF..GGPQ.DA
Retrocopy QDQGAVLPIRVHTIVISVQHDEKVCLDEMRDALKKKVIKAVVPAKYLVEYTIYHLQPSGRFTVGGPQVDA

Parental  GLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLS
          GLTG.KI.VDTY.G..AHGGGAFSG.DYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSY..G.SH.LS
Retrocopy GLTGWKITVDTYRGCRAHGGGAFSGTDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYTFGLSHVLS

Parental  ISIFHYGTSQKSERELLEIVKKNFDLRP-GVIVRDLDLKKPIYQRTAAYGHFGR-DSFPWEVPKKLKY
          ISIFHYGTSQKSERELLE.VKKNFDL.P...IVRDLDLKKPIYQRTAA.GHFGR.DSFPWE.P.KLKY
Retrocopy ISIFHYGTSQKSERELLETVKKNFDLHP>RIIVRDLDLKKPIYQRTAA*GHFGR<DSFPWELPQKLKY

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_1580 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013959	1 retrocopy	retro_chof_30,
Echinops telfairi	ENSETEG00000007634	2 retrocopies	retro_etel_1308, retro_etel_1532,
Echinops telfairi	ENSETEG00000015680	4 retrocopies	retro_etel_1669, retro_etel_1813, retro_etel_597, retro_etel_977,
Ornithorhynchus anatinus	ENSOANG00000003060	1 retrocopy	retro_oana_84,
Otolemur garnettii	ENSOGAG00000026925	1 retrocopy	retro_ogar_1580 ,
Rattus norvegicus	ENSRNOG00000013520	2 retrocopies	retro_rnor_2032, retro_rnor_955,