RetrogeneDB ID: retro_ogar_3448

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873845.1:390406..391152(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEAD2
• Ensembl ID: ENSOGAG00000010067
• Aliases: None
• Description: TEA domain family member 2 [Source:HGNC Symbol;Acc:11715]

Sequence

>retro_ogar_3448
CCAGGGTATGGGTCCACTTAACCCCTCTCACCCCTGCCTCTAACTGCCCCATTACCCCCAGCACAGCAGGCTTGGGCCCT
GGGCACTGTGTGGTTGTAGCTAGTAGAGTTCTTGGCCTGTGTGGAACTGCCAAATGGACCTGATTCATATCAAAGTCACC
TGTTTGTACACATCACCCAGCATTGCCCTGGAGTCCCCCTACTCAAGAGTGTGGATGTCCAGCAGATCAATTACAAATTC
CCTGAGAAAAGGGTGGTCTACAAGAACTGAAGATCATGGCTTCCCCAACATCTTTTTCCTGGTCAAGTTCTGGGCAGACC
TGAACTGAGGCCCAAGTGGTGAGGAGGCCAGGGCTAGCAGTGGCAGCAGCAGTAACAGTGGTGGCTTTGACAGATGAGCA
GCCAGTATGAGAGCCTGGGGCACATGACCCTCAAGTGCTTCTCCAAGGTCTGCTCCTTTGGCAAGCAGGTGGTGGAGAAG
GTAGAGACAGAGTGGGCCCAGGTGGAGGATGGAGATTTGTGTACTGCCTGTTGAGCTCACCCCTCTGAGAGTACCTGGTG
AATTTCCTGCACAAGTTGTGGCAGCTGGCTGAGTGATACATGATGAACAGCATCCTTGAAAACTTCGCCATCCTCCAGGT
GGTGACAGACAGAGACACCCAGGAATTTCTGCCGTGTACCACTTATGTCTTTAAGGTCTCCACCAGTGAACACAGGGCCC
ACCACATTTACTGCCTGGTCTAGGAC

Alignment

ORF - retro_ogar_3448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.37 %
• Parental protein coverage: 56.35 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PGYEASQSLSPLPPPAPSPPAWQARALGTARLQLVEFSAFVEPPDAVDSYQRHLFVHISQHCPSPGAPPL
          PGY.....LSPLP..AP.PPA.QA.ALGT..L.LVEF.A.VE.P...DSYQ.HLFVHI.QHCP..G.P.L
Retrocopy PGYGST*PLSPLPLTAPLPPAQQAWALGTVWL*LVEFLACVELPNGPDSYQSHLFVHITQHCP--GVPLL

Parental  ESVDVRQIYDKFPEK-KGGLRELY-DRGPPHAFFLVKFWADLNWGPSGEEAGAGSGSNSSSGGFYG-VSS
          .SVDV.QI..KFPEK.KGGL.EL..D.G.P..FFLVKFWADLN.GPSGEEA.A.SGS.S.SGGF....SS
Retrocopy KSVDVQQINYKFPEK<KGGLQELK<DHGFPNIFFLVKFWADLN*GPSGEEARASSGSSSNSGGFDR<MSS

Parental  QYESLEHMTLTCSSKVCSFGKQVVEKVETERAQLEDG-RFVYRLLRSPMCEYLVNFLHKLRQLPERYMMN
          QYESL.HMTL.C.SKVCSFGKQVVEKVETE.AQ.EDG.RFVY.LL.SP..EYLVNFLHKL.QL.E.YMMN
Retrocopy QYESLGHMTLKCFSKVCSFGKQVVEKVETEWAQVEDG<RFVYCLLSSPL*EYLVNFLHKLWQLAE*YMMN

Parental  SVLENFTILQVVTNRDTQELLLCTAYVFEVSTSERGAQHHIYRLVRD
          S.LENF.ILQVVT.RDTQE.L.CT.YVF.VSTSE..A.HHIY.LV.D
Retrocopy SILENFAILQVVTDRDTQEFLPCTTYVFKVSTSEHRA-HHIYCLV*D

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_3448 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000016184	1 retrocopy	retro_lafr_1143,
Otolemur garnettii	ENSOGAG00000010067	2 retrocopies	retro_ogar_2638, retro_ogar_3448 ,
Rattus norvegicus	ENSRNOG00000020695	1 retrocopy	retro_rnor_1929,