RetrogeneDB ID: retro_ogar_2236

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873605.1:396348..397032(+)
• Located in intron of: ENSOGAG00000017247

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFRD2
• Ensembl ID: ENSOGAG00000012534
• Aliases: None
• Description: interferon-related developmental regulator 2 [Source:HGNC Symbol;Acc:5457]

Sequence

>retro_ogar_2236
AGAAAGGGCCATGCGCCCCACAAGGGCAGCCAGCACCGTGGAGGAGGTGTCCAGAGCAGTGCCAAAGCTGACCTGGGTTC
TAGTGAGGCCCACAGCACCACCAGTGAGTGCCCCGGCCTTCTCAGCACCACTGCAGAGGACAGCCTTGGGGGGATGTCAT
GGATAAGCAGGGCTGGCAGGAAGACCTCCAGGAAAAAGCTGAAGGTTTTTGTGGACTGCCTTGCAGATGAGAGTGCCAAG
GACCCTGCAAGATACTCTGTGGGACGTGTTGGTCCTGGAGTCCTACCTGCTCCCTGGCATCTTGCTAGAGCGCTGCCTTA
TTCTGGCCAATGTCCTGGAAAAGTACCTCAAGAAAGGGAAAGGGTGAGGAATAGTCCCTGGCTGCTGCCATGCTAGGCCT
GGTCTGTGTGTGGCTGGGCCCTGGACCCAAAGGTGAAGAGGAGTTCCACAGCCTGCAGTCTCTGCTAGTCTCTGTGCTCA
GGGCCAATACAGCCAGCCCTGCTACCTGGCTCCACTGTGCTTCTGCTCTTGGCCTGGGCTGCTGCGTGGTTGCTGCTGAC
ATCCAGGACTTGGGCTCTTGTTTTGCCTGCTTAGTGTTTTCAGCTGGACCTCTGGTGGCTCCACAGCCCAGTAGTGCCTC
CCAGTCTGCAGGGCCTGCTCTGTGCTTCCCTGCAGGCCTGGGCA

Alignment

ORF - retro_ogar_2236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.98 %
• Parental protein coverage: 52.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RKGSRRRGGGVQSSAKADSGSSEDEAASEARSITSECPSLLSTTAEDSLGG-DVVDEQGQQEDLEEK-LK
          RKG.....G.........S....D...SEA.S.TSECP.LLSTTAEDSLGG.DV.D.QG.QEDL.EK.LK
Retrocopy RKGHAPHKGSQHRGGGVQSSAKADLGSSEAHSTTSECPGLLSTTAEDSLGG<DVMDKQGWQEDLQEK>LK

Parental  EYVDCLTDKSAK-TRQGALESLRLALASHLVPDFLLERLLTLADALEKCLKKGKG-EEQALAAAILGLVC
          ..VDCL.D.SAK.T.Q..L....L.L.S.L.P..LLER.L.LA..LEK.LKKGKG.EE..LAAA.LGLVC
Retrocopy VFVDCLADESAK>TLQDTLWDV-LVLESYLLPGILLERCLILANVLEKYLKKGKG>EE*SLAAAMLGLVC

Parental  VQLGPGPKGEEVFHSLQPLLVSVLSDSTATPAARLHCASALGLSCYVAATDIQDLVSCLTCLESVFSRSR
          V.LGPGPKGEE.FHSLQ.LLVSVL...TA.PA..LHCASALGL.C.V.A.DIQDL.SC..CL..VFS...
Retrocopy VWLGPGPKGEEEFHSLQSLLVSVLRANTASPATWLHCASALGLGCCVVAADIQDLGSCFACL--VFSAGP

Parental  VGSTVP-VVPTSLHGLLCAALQAWA
          .....P.VVP.SL.GLLCA.LQAWA
Retrocopy LVAPQP>VVPPSLQGLLCASLQAWA

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_2236 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004993	1 retrocopy	retro_cjac_4213,
Macaca mulatta	ENSMMUG00000020119	1 retrocopy	retro_mmul_1073,
Otolemur garnettii	ENSOGAG00000004194	1 retrocopy	retro_ogar_695,
Otolemur garnettii	ENSOGAG00000012534	1 retrocopy	retro_ogar_2236 ,
Sus scrofa	ENSSSCG00000024363	1 retrocopy	retro_sscr_445,