RetrogeneDB ID: retro_ttru_1118

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_103913:2492..3247(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBX2
• Ensembl ID: ENSTTRG00000013787
• Aliases: None
• Description: pre-B-cell leukemia homeobox 2 [Source:HGNC Symbol;Acc:8633]

Sequence

>retro_ttru_1118
GAGGCCCAGGCCAAGAAACACGTCCTAAACTGCCACCAAATGAAGCCTGCTCTCATTAACGTCCTTCGTGAAATTGAGGA
GAAAACCGCCCTCAGCATTCGAAACTCCCAAGAGGAAGAGCCTGTGGACCTACAGCTGATGCACTTGGACACCATGCTTC
TGGCAGAGGTTGTGGCCGACCCCGAGAAAGGGGATGGCTCAGGGTCAGCAGCTGCCACCACTGCAGCCTCCTGGGGAGGT
GTGTCCCCTAACAACCCCATCGAACACTTGGACTATCGCAGCAAACTTGCCCAGGTCCGCCACATGTACCACTCGGAGCT
GGAGAAGTATGAGAAGGCACGAAGCAAGTTCACAGCCCACGTCCTGAAACTGCTGAGGGAGCAAAGCCGCACGCAGTTCA
TAGCACCCAAGGAGACGGAGCACATGGTGAGCGTCATCCGCCGGAAGTTCAGCGTCATCCAGAGGCAACTCAAGCAGAGC
CCCTGCAAGGCGGCGATGATCCTGCATTCTGGTTCCTGGATGCCGGACGAAAAAACCGTAACTTCAGCAAACAGGCCACT
GAGGTCCCGAATGAGTGTTTCTACTCCCACCTGAGTAACTCATATCCTAGTGACGAGGCTAAGGAGGAGCTTGCCAAGAA
GTGTGGAATCACTGCCTCTCAGGTCCCCAACTGGTTTGGCAACAAGCAGATGCGCTATAAGAAAAATACTGGAAAGTTCC
AAGAGGAGGCAAACATCTAGGCCATCAAGACCGCT

Alignment

ORF - retro_ttru_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.28 %
• Parental protein coverage: 62.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EAQAKKHALNCHRMKPALFSVLCEIKEKTGLSIRSSQEEEPVDPQLMRLDNMLLAEGVAGPEKGGGSAAA
          EAQAKKH.LNCH.MKPAL..VL.EI.EKT.LSIR.SQEEEPVD.QLM.LD.MLLAE.VA.PEKG.GS..A
Retrocopy EAQAKKHVLNCHQMKPALINVLREIEEKTALSIRNSQEEEPVDLQLMHLDTMLLAEVVADPEKGDGSGSA

Parental  AAAAAASGGGVSPDNSIEHSDYRSKLAQIRHIYHSELEKYEQACNEFTTHVMNLLREQSRTRPVAPKEME
          AA..AAS.GGVSP.N.IEH.DYRSKLAQ.RH.YHSELEKYE.A...FT.HV..LLREQSRT...APKE.E
Retrocopy AATTAASWGGVSPNNPIEHLDYRSKLAQVRHMYHSELEKYEKARSKFTAHVLKLLREQSRTQFIAPKETE

Parental  RMVGIIHRKFSAIQMQLKQSTCEAVMILRSR-FLDARRKRRNFSKQATEVLNEYFYSHLSNPYPSEEAKE
          .MV..I.RKFS.IQ.QLKQS.C.A.MIL.S..FLDA.RK.RNFSKQATEV.NE.FYSHLSN.YPS.EAKE
Retrocopy HMVSVIRRKFSVIQRQLKQSPCKAAMILHSG<FLDAGRKNRNFSKQATEVPNECFYSHLSNSYPSDEAKE

Parental  ELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAVKTA
          ELAKKCGIT.SQV.NWFGNK..RYKKN.GKFQEEANI.A.KTA
Retrocopy ELAKKCGITASQVPNWFGNKQMRYKKNTGKFQEEANI*AIKTA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1118 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1118 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 ,