RetrogeneDB ID: retro_ogar_1805

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873566.1:9868051..9869197(-)
• Located in intron of: ENSOGAG00000000061

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGAT4A
• Ensembl ID: ENSOGAG00000011487
• Aliases: None
• Description: mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A [Source:HGNC Symbol;Acc:7047]

Sequence

>retro_ogar_1805
ATGAGGCTCGGAAATGGAACTGTGGCCCCTACTTTAGCATTTATCATTTCGTTCCTTACTCTCTCTTGGTATACCACACA
GCAAAATGGGAAAGAAAAACTTATTGCTTATCGATGAGAATTTCTCGCTTTGAAAGAACGTCTTCGAATAGCTGAGCATA
GAATCTCTCAGCGCTCTTCTGAATTAAATACCATTGTACAACAGTTCAGACGTGTAGGAGCCGAAACAAATGGAAGTAAG
GATACAGTGAATAAGTTTTCAGGTAATACCCTAAGGCTGCTAAAGGAATTAACAAGCAAAAAATCTCTTCAAGTGCCAGG
TATTTATTATCATTTGCCTCATTTATGGCAAAATGAAGGAAGCCTTCAACCTGCAGTGCAGATTGGCAGCGGAAGAACAG
GAGTTTCGATAGTAATGGGAATCCCCACAGTGAAGAGAGAAGTTAGATCAGACCTCATAGAAACTCTTCATCCCCTTATC
AATAACCTGTATCCTGAAGAGAAGGTGGACTGTGTCATAGTAGTCTTCATAGGAGAGACAGATATTGATTATGTGCATGG
TGTTGTTGCCAACCTGGAGAAACAATTTTCTAAAGAAATCTGTTCTGGCCTGGTAGAAGTAATATCACCCCCTGAGAGCT
ATTATCCGGACTCAACAAACCTGAAGGAGACATTTGGAGATTCTAAAGAAGGAGTAAGATGGAGAACAAAACAAAACCTG
GATTACTGTTTTCTAATGATGTATGCTCAGGAAAAGGGCATATATTACATTCAGCTTGAAGAGGATATCATTGTCAAACA
GAATTATTTTAATACTATAAAAAAATTTGCACTTCAGCTTTCTTCTGAGGAATGGATGATTCTAGAGTTTTCCCAACTGG
GCTTCATTGGTAAAATATTTCAAGCACCGGACCTCACTCTGATTGTAGAATTCATGTTCTATAAGGAGAAACCCATCGAC
TGGCTTTTGGATCCTATTCTCTGGGTGAAAGTCTGCAACCCTGAAAAAGATGCAAAACATTGTGATAGACAAAAAGCAAA
TCTGCGAATTCGCTTCAGACCTTCCCTTTGCCAACATGTTGGTCTGCATTCATCACTGTCAGGAAAAATCCAGAAACTCG
TGGATACGGATTATATGAAACCATTA

Alignment

ORF - retro_ogar_1805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.27 %
• Parental protein coverage: 71.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRSRNGQVGTRAPFFFFFLRRTLITFLVLLLEKLIAYQREFLALKERLRIAEHRISQRSSELNSIVQQFR
          .R..NG.V.....F...FL.....T......EKLIAY..EFLALKERLRIAEHRISQRSSELN.IVQQFR
Retrocopy MRLGNGTVAPTLAFIISFLTLSWYTTQQNGKEKLIAYR*EFLALKERLRIAEHRISQRSSELNTIVQQFR

Parental  RVGAETNGSKDTVNKFSDNTVKLLKELLTSKKSLQVPSIYYHLPHLLQNEGSLQPAVQIGSGRTGVSIVM
          RVGAETNGSKDTVNKFS.NT..LLKEL.TSKKSLQVP.IYYHLPHL.QNEGSLQPAVQIGSGRTGVSIVM
Retrocopy RVGAETNGSKDTVNKFSGNTLRLLKEL-TSKKSLQVPGIYYHLPHLWQNEGSLQPAVQIGSGRTGVSIVM

Parental  GIPTVKREVRSYLIETLHSLIDNLYPEEKMDCVIVVFIGETDIDYVHGVVANLEKEFSKEISSGLVEVIS
          GIPTVKREVRS.LIETLH.LI.NLYPEEK.DCVIVVFIGETDIDYVHGVVANLEK.FSKEI.SGLVEVIS
Retrocopy GIPTVKREVRSDLIETLHPLINNLYPEEKVDCVIVVFIGETDIDYVHGVVANLEKQFSKEICSGLVEVIS

Parental  PPESYYPDLTNLKETFGDSKERVRWRTKQNLDYCFLMMYAQEKGIYYIQLEDDIIVKQNYFNTIKNFALQ
          PPESYYPD.TNLKETFGDSKE.VRWRTKQNLDYCFLMMYAQEKGIYYIQLE.DIIVKQNYFNTIK.FALQ
Retrocopy PPESYYPDSTNLKETFGDSKEGVRWRTKQNLDYCFLMMYAQEKGIYYIQLEEDIIVKQNYFNTIKKFALQ

Parental  LSSEEWMILEFSQLGFIGKMFQAPDLTLIVEFIFMFYKEKPIDWLLDHILWVKVCNPEKDAKHCDRQKAN
          LSSEEWMILEFSQLGFIGK.FQAPDLTLIVE..FMFYKEKPIDWLLD.ILWVKVCNPEKDAKHCDRQKAN
Retrocopy LSSEEWMILEFSQLGFIGKIFQAPDLTLIVE--FMFYKEKPIDWLLDPILWVKVCNPEKDAKHCDRQKAN

Parental  LRIRFRPSLFQHVGLHSSLSGKIQKLTDKDYMKPL
          LRIRFRPSL.QHVGLHSSLSGKIQKL.D.DYMKPL
Retrocopy LRIRFRPSLCQHVGLHSSLSGKIQKLVDTDYMKPL

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_1805 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000011487	1 retrocopy	retro_ogar_1805 ,
Rattus norvegicus	ENSRNOG00000018276	2 retrocopies	retro_rnor_600, retro_rnor_601,