RetrogeneDB ID: retro_ogar_2252

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873606.1:351432..352591(-)
• Located in intron of: ENSOGAG00000000134

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBX2
• Ensembl ID: ENSOGAG00000016303
• Aliases: None
• Description: pre-B-cell leukemia homeobox 2 [Source:HGNC Symbol;Acc:8633]

Sequence

>retro_ogar_2252
GTCCCAGGAGGTCAAGGGAAGCAAGACATCGGGGACATTCTGCCCCAGATAATGATCATCGCCCACCAGAGCCTGGACAA
GACCCAGGCCAAGAAACACACCCTAAACTGCCACCAAATGAAGCCTGCTCTCTTTAGCGTCCTGTGTGAAATCAAGGAGA
AAACTGGCCTCAGCATTCCAAGCTCCCAAGAGGAGGAGCTGGTGGACCCACAGCTGAAGCGCTTGGACAACATGCTTTTG
GCAGAGGGTGTGGCTAGGCCTGAGAAAGGGGGGCTCAGCAGCAGCTACTGCAGCTGCTGCAGCATCCGGGGGCAGTGTGT
CCCCTGACAACTCCATCGAACACTCAGACTATTGCAGCAAACTTGCCCAGATCTGCCACATCTACCATTCAGAGCTGGAG
AACTATGAACAGGCATGTAATGAGTTCATAACTCATGTCATGAACCTGCTGAGGAAGCAGAGGTGCACAAGGCCAGTGGC
ACCCAGAGTGATGGAGCGCATGGTAAGCATCATCCATCGAAAGTTCAATGCCATCCAGATGCAGCTCAAGCAGAGCACCT
GTGAGGCCGTCATGCGCCTACGTTCCTGCTTCCTGGTTGCCAGATGAAAGCACTATAACTTCAGCAAACAGGCCACTGAG
GTCCTAAATGAGTATTTCTATTCCCACCTGAGTAACCCATATCCTAGTGAGGAGGCGAAGGAGGAGCTCGCTAAGAAATG
CGGCATCACTGTCTCTCAGGTCTCCAACTGGTTTGGCAACAAGCGCATTCGCTATAAAAAAAATATTGGAAAGTTCCATG
AGGAGGCAAACATCTATGCTGTCAAGACTGCTGTGTCAGACACATGGGAGGCCACAGCCTCACCAGCTCCCTGACACCCC
CTTCCTCTGCAGGCTCTGGCGGCTCTTTCAATCTCTCAGGATCCGGAGACATGTTCTTGGGGATGCCTGGGCTCAATGGA
GATTCCTATTCTGCTTCCCAGGTAGAAATCATTCCAACAGTCAGTGGGGCCAGGGGGCCATGGAGATAACCTCGGGGCAG
GCCAGATGTACAGCCCTCAGGAAATGAGGGCAAATGGCAGTTGGCAGGAGGCTGTGACCCCCTCTTCGGTGACATTGCCA
ACAGAGGGACCAGGGAGTGTTCACTCTGACACCTCCAGC

Alignment

ORF - retro_ogar_2252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.9 %
• Parental protein coverage: 90. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPGGRGKQDIGDILQQIMTITDQSLDEAQAKKHALNCHRMKPALFSVLCEIKEKTGLSIRSSQEEEPVDP
          VPGG.GKQDIGDIL.QIM.I..QSLD..QAKKH.LNCH.MKPALFSVLCEIKEKTGLSI.SSQEEE.VDP
Retrocopy VPGGQGKQDIGDILPQIMIIAHQSLDKTQAKKHTLNCHQMKPALFSVLCEIKEKTGLSIPSSQEEELVDP

Parental  QLMRLDNMLLAEGVA-GPEKGGGSAAAAAAAAASGGGVSPDNSIEHSDYRSKLAQIRHIYHSELEKYEQA
          QL.RLDNMLLAEGVA.G..KGG.SAAA.AAAAASGG.VSPDNSIEHSDY.SKLAQI.HIYHSELE.YEQA
Retrocopy QLKRLDNMLLAEGVA>GLRKGG-SAAATAAAAASGGSVSPDNSIEHSDYCSKLAQICHIYHSELENYEQA

Parental  CNEFTTHVMNLLREQSRTRPVAPKEMERMVSIIHRKFSAIQMQLKQSTCEAVMILRSRFLDARRKRRNFS
          CNEF.THVMNLLR.Q..TRPVAP..MERMVSIIHRKF.AIQMQLKQSTCEAVM.LRS.FL.AR.K..NFS
Retrocopy CNEFITHVMNLLRKQRCTRPVAPRVMERMVSIIHRKFNAIQMQLKQSTCEAVMRLRSCFLVAR*KHYNFS

Parental  KQATEVLNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAVKTAV
          KQATEVLNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRY...IGKF.EEANIYAVKTAV
Retrocopy KQATEVLNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYXXXIGKFHEEANIYAVKTAV

Parental  SVT-QGGHSRTSSPTPPSSAGSGGSFNLSGSGDMFLGMPGLNGDSYSSSQVE-SLRHSMGPGSYGDNLGA
          S.T..GGHS.TSS.TPPSSAGSGGSFNLSGSGDMFLGMPGLNGDSYS.SQVE.S...S.GPG..GDNLGA
Retrocopy SDT<MGGHSLTSSLTPPSSAGSGGSFNLSGSGDMFLGMPGLNGDSYSASQVE>SFQQSVGPGGHGDNLGA

Parental  GQIYSPREMRANGSWQEAVTPSSVTSPTEGPGSVHSDTSN
          GQ.YSP.EMRANGSWQEAVTPSSVT.PTEGPGSVHSDTS.
Retrocopy GQMYSPQEMRANGSWQEAVTPSSVTLPTEGPGSVHSDTSS

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_2252 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000000548	3 retrocopies	retro_mluc_1220, retro_mluc_1790, retro_mluc_981,
Otolemur garnettii	ENSOGAG00000016303	1 retrocopy	retro_ogar_2252 ,
Tursiops truncatus	ENSTTRG00000013787	1 retrocopy	retro_ttru_1118,