RetrogeneDB ID: retro_ogar_3188

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873738.1:2031313..2032241(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSOGAG00000002488
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9300]

Sequence

>retro_ogar_3188
GACAGCAAGGCGTTCACCAAGGAGCTGGACCAAGTAGGTCGAACAGCTGAATGAGTGTAAACAGCTTAATGAATACCAAG
TGCGGACGCTGTGCAAAAAGGCTAAAGAAATTCTTACAAAAGAATCAAATGTGCAGGAGGTTTGATGTTCTGTTACTGTC
TGTGGAGATGTGCATGGCAAATTTCATGATCTTATGGAACTCTTTAGAATTGGTGGGAAATCACCAGATACAAACTATTT
ATTCATGGGCGACTACGGAGACAGAGGTTATTATTCAGTGGAGACTGTCACTCTTCTTGTAGCATTAAAGGTGCATTATC
CAGAATGCATTACAATATTGGGAGGAAATGATGAAAGCTGACAAATTACCCAAGTATATGGCTTTTATGATGAATGTCTA
CAAAAGTATGGGAATGCCAATGTTTGGAAATATTTTACCCATCTATTTGATTATCTCCCACTTACAGTTTTAGTACATGG
ACAGACAGATACTCTGCCTCCATGGTGGTCTCTCTCCATCCATAGACACACTGGATCATATAAGAACCCTGGATCGCTTG
CAGGAAGTACCACATGAGGGCCCAATGTGTGATCTGTTATGGTCAGATCCAGATGATCGTGGTGGGTGGGGTATTTCACC
ATGTAGTGCTGGCTACACATTTGGACAAGACATTTCTGAAATATTTAACCATGCCAATGGCCTCACTCTGGTTTCTCGTG
CTCACCAGCTTGTAATGGAGGGGTACAATTGGTGTTATGATCGGAATGTGGTTCCAATTTTCAGTGCACCCAATTACTGT
TATCGTTGTGGGAACCAGGCTGCTATCACGGAATTAGACGACTCTTTAAAGTATTCCTTCCTTCAGTTTACCCAACACCT
CTTTGTGGAGAGCCTCACGTTACACGGCACACCCCAGACTATTTCCTG

Alignment

ORF - retro_ogar_3188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.69 %
• Parental protein coverage: 99.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDKAFTKELDQW-VEQLNECKQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
          D.KAFTKELDQ..VEQLNECKQLNE.QVRTLC.KAKEILTKESNVQEV.C.VTVCGDVHG.FHDLMELFR
Retrocopy DSKAFTKELDQV>VEQLNECKQLNEYQVRTLCKKAKEILTKESNVQEV*CSVTVCGDVHGKFHDLMELFR

Parental  IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNA
          IGGKSPDTNYLFMGDY.DRGYYSVETVTLLVALKV.YPE.ITIL.GN.ES.QITQVYGFYDECL.KYGNA
Retrocopy IGGKSPDTNYLFMGDYGDRGYYSVETVTLLVALKVHYPECITILGGNDES*QITQVYGFYDECLQKYGNA

Parental  NVWKYFTDLFDYLPLTALVDGQV-CIC--GGFTPSPGQTATIKTLTRKNIFLVQGPMCDLLWSDPDDRGG
          NVWKYFT.LFDYLPLT.LV.GQ....C..GG..PS......I.TL.R.......GPMCDLLWSDPDDRGG
Retrocopy NVWKYFTHLFDYLPLTVLVHGQT>ILCLHGGLSPSIDTLDHIRTLDRLQEVPHEGPMCDLLWSDPDDRGG

Parental  WGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMEL
          WGISP..AGYTFGQDISE.FNHANGLTLVSRAHQLVMEGYNWC.DRNVV.IFSAPNYCYRCGNQAAI.EL
Retrocopy WGISPCSAGYTFGQDISEIFNHANGLTLVSRAHQLVMEGYNWCYDRNVVPIFSAPNYCYRCGNQAAITEL

Parental  DDTLKYSFLQFD-PAPRRGEPHVTRRTPDYFL
          DD.LKYSFLQF..P.P..GEPHVTR.TPDYFL
Retrocopy DDSLKYSFLQFT<PTPLCGEPHVTRHTPDYFL

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_3188 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001615	1 retrocopy	retro_amel_663,
Bos taurus	ENSBTAG00000009245	3 retrocopies	retro_btau_1199, retro_btau_1750, retro_btau_704,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Echinops telfairi	ENSETEG00000018123	4 retrocopies	retro_etel_1607, retro_etel_1923, retro_etel_680, retro_etel_702,
Felis catus	ENSFCAG00000025139	1 retrocopy	retro_fcat_1884,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,
Otolemur garnettii	ENSOGAG00000002488	1 retrocopy	retro_ogar_3188 ,
Otolemur garnettii	ENSOGAG00000009695	2 retrocopies	retro_ogar_3414, retro_ogar_921,
Tursiops truncatus	ENSTTRG00000000102	1 retrocopy	retro_ttru_1576,