RetrogeneDB ID: retro_ttru_1424

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112927:86555..87402(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C3orf38
• Ensembl ID: ENSTTRG00000002941
• Aliases: None
• Description: chromosome 3 open reading frame 38 [Source:HGNC Symbol;Acc:28384]

Sequence

>retro_ttru_1424
GTTGAGAAGTCGGGGCTCAGCTACCCAGAGATGGAGGGCTGTCGTAACCTGCTCGGCCTATTGGACAACGACGAGATCAT
GGCCCTATGCGATACCATCACCAACCGCCTGGTGCAGCCTGAGGACCACCAAGATGCCATTCGTGAAATATTAGTGTACA
GTCAAGGTGCAGAAGAACTTTTGAGGCGTAAAACAGTCCACCGAGAAATCATATTTAAGTACTTGGCGACACAGTGGGTT
ATTCTACCTCCAGCTACTGAAAAACACAACCTTATTCAGCATGCGAAGGATTACTAGAAAGAGCAGTCACAACTGAAACT
GAAGGAAGTGGCAGGGCCAGTTGAGACAGAGGACATGAGACTCTCTGAACAGCAGGAGGAAAAAGATAGAAAAGCTGAAA
AGTTTGCTTTTCGTCGATTAGGCGCAGAATTCTGTCACTGGTGCTCTGCACTTCTTAATTCTCAGAATGCTATTCTGGGA
CCACGTCAAGAAGAATGGGGGCCACAGCACTTCTGGCATGACGTCAAGCTTACGTTCTATTACCACACATCTGAAACAAA
ATGTGATAGACCACCATGGAGCAGAAATTGTGAGACTTCGTCTGCTGTCACTAGTGAATGAAGAATAACTTTTTCTCAGT
CCCAACCTAAATTCCCATGGACTGAAATGCACTTCTCCCCATGGTCTCATTATGGTTTAGAGTTTGCTGGGACTGTCCAC
CGAGGGAACACCTGTTGGGGCATTTTTGAACAGATTTTTGGACTCCTCCACTGCCCCTTTGTGGAGAATACTTTGGAAAA
TCAAACGTGTCAACCTGAGAATTACAGCAGAGAGTTCCCTTGCTCCC

Alignment

ORF - retro_ttru_1424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.25 %
• Parental protein coverage: 86.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VEMSGLSYSEMEGCRSLLGLLDNDEIMALCDTITNRQVQPEDRQDAIHAILVYSQSVEELLRRKKVHREI
          VE.SGLSY.EMEGCR.LLGLLDNDEIMALCDTITNR.VQPED.QDAI..ILVYSQ..EELLRRK.VHREI
Retrocopy VEKSGLSYPEMEGCRNLLGLLDNDEIMALCDTITNRLVQPEDHQDAIREILVYSQGAEELLRRKTVHREI

Parental  IFKYLATQGVIIPPATEKHNLIQHAKDYWKKQSQLKLKETPEPVKTEDIRLFEQQEKEDKKAENVDFRRL
          IFKYLATQ.VI.PPATEKHNLIQHAKDY.K.QSQLKLKE...PV.TED.RL.EQQE..D.KAE...FRRL
Retrocopy IFKYLATQWVILPPATEKHNLIQHAKDY*KEQSQLKLKEVAGPVETEDMRLSEQQEEKDRKAEKFAFRRL

Parental  GEEFCHWFFELLNSQNPLLGPPQDEWGPQHFWHDVKLRFYYNTSE-QNVIDYHGAEIVSLRLLSLVKEEY
          G.EFCHW...LLNSQN..LGP.Q.EWGPQHFWHDVKL.FYY.TSE.QNVID.HGAEIV.LRLLSLV.EE.
Retrocopy GAEFCHWCSALLNSQNAILGPRQEEWGPQHFWHDVKLTFYYHTSE>QNVIDHHGAEIVRLRLLSLVNEE*

Parental  LFLSPNLDSHGLKCAA-SPHGLVMVGVAGTVHRENTCLGIFEQIFGLIRCPFVENT-WKIKFINLRIIGE
          LFLSPNL.SHGLKC...SP........AGTVHR.NTC.GIFEQIFGL..CPFVENT.WKIK..NLRI..E
Retrocopy LFLSPNLNSHGLKCTS<SPWSHYGLEFAGTVHRGNTCWGIFEQIFGLLHCPFVENT>WKIKRVNLRITAE

Parental  SSLAP
          SSLAP
Retrocopy SSLAP

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_1424 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1424 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000059920	3 retrocopies	retro_mmus_2986, retro_mmus_376, retro_mmus_695,
Tursiops truncatus	ENSTTRG00000002941	1 retrocopy	retro_ttru_1424 ,