RetrogeneDB ID: retro_ttru_963

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_832:54306..55295(-)
• Located in intron of: ENSTTRG00000009304

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFB1M
• Ensembl ID: ENSTTRG00000006327
• Aliases: None
• Description: transcription factor B1, mitochondrial [Source:HGNC Symbol;Acc:17037]

Sequence

>retro_ttru_963
ATGGCCGCCTCCAGGACGCTCGGCCCCTTCCATCTCCCACCATTACCCACAATTCGAGAAATCATTAAGTTGTTTAGACT
GCAAGCTGTGAAGCAGCTATCCCAGAATTTTCTCTTGGACTTGAGGCTGACAGATAAAATTGTAAGGAAAGCTGGCAGTC
TGACAAATGCTTATGTTTATGAAGTGGGCCCTGGGCCTGGGGGAATCACAAGATCCATTCTCAATGCCGGTGTTGCTGAA
CTTCTGGTGGTTGAAAAGGATAGTCGATTTATTCCTGGATTACAGATGCTTTCTGATGCAGCACCTGGAAAACTGAGAAT
TGTCCATGGAGATGTCTTGACATTTAAGATAGAAAGGGCTTTTCCAGAAAATCTCAAAAGACAGTGGGAGGATGATCTTC
CAAATGTACATATTATTGGAAATCTGCCTTTTAGTGTATCAACTCCACTGATTATCACATGGCTTGAAAATGTTTCTCAT
AGAAATGGACCTTTTGCTTATGGCAGAACCCAGATGACTTTTCAAAAGGAAGTGGCAGAGAGACTTACAGCCAGTACGGG
AAGCAAGCAGCGTAGCCGCCTCTCCATCATGGCCCAGTACCTCTGCGACGTTCAGCACATCTTGACAGTTCCAGGTCAGG
CTTTCATCCCCAAACCAGAGGTGGACTCGGGGGTGGTGCATTTCACCCCCCTGACCCGGCCCAGGATAGAGCAGCCATTC
AGGCTGGTGGAGAGAGTCGTTCAGAATGCCTTTCAGTTCCGAAGGAAATACTGCCATCGAGGGCCTGGAATGTTATTCCC
TGAAGCCCGGCGATTAGAAAGCACTGGGAAACTGTTCCGCTTGGCAGATGTGGACCCTACCCTTCGACCCACCAGCTCTC
TGTCTTACATTTTAAGAGCCTCTGTGACGCATACCGAAAAATGTGTGATGAAGACCCACACCACTTTGCTTACAATTTCA
GAGAAGAACTCAAGCAAAAATCAGAAAAA

Alignment

ORF - retro_ttru_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.39 %
• Parental protein coverage: 98.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASRTLGTFRLPPLPTIREIIKLFRLQAVKQLSQNFLLDLRLTDKIVRKAGSLTNAYVYEVGPGPGGIT
          MAASRTLG.F.LPPLPTIREIIKLFRLQAVKQLSQNFLLDLRLTDKIVRKAGSLTNAYVYEVGPGPGGIT
Retrocopy MAASRTLGPFHLPPLPTIREIIKLFRLQAVKQLSQNFLLDLRLTDKIVRKAGSLTNAYVYEVGPGPGGIT

Parental  RSILNAGVAELLVVEKDGRFIPGLQMLSDAAPGKLRIVHGDVLTFKIENAFPESLKRQWEDDPPNVHIIG
          RSILNAGVAELLVVEKD.RFIPGLQMLSDAAPGKLRIVHGDVLTFKIE.AFPE.LKRQWEDD.PNVHIIG
Retrocopy RSILNAGVAELLVVEKDSRFIPGLQMLSDAAPGKLRIVHGDVLTFKIERAFPENLKRQWEDDLPNVHIIG

Parental  NLPFSVSTPLIIKWLENVSQRNGPFAYGRTQMTLTFQKEVAERLTASTGSKQRSRLSIMAQYLCDVQHIL
          NLPFSVSTPLII.WLENVS.RNGPFAYGRTQM..TFQKEVAERLTASTGSKQRSRLSIMAQYLCDVQHIL
Retrocopy NLPFSVSTPLIITWLENVSHRNGPFAYGRTQM--TFQKEVAERLTASTGSKQRSRLSIMAQYLCDVQHIL

Parental  TIPGQAFIPKPEVDSGVVHFTPLTQPRIEQPFKLVERVVQNAFQFRRKYCHRGLGMLFPEAQRLESTGKL
          T.PGQAFIPKPEVDSGVVHFTPLT.PRIEQPF.LVERVVQNAFQFRRKYCHRG.GMLFPEA.RLESTGKL
Retrocopy TVPGQAFIPKPEVDSGVVHFTPLTRPRIEQPFRLVERVVQNAFQFRRKYCHRGPGMLFPEARRLESTGKL

Parental  LQLADVDPTLRPT-QLSVLHFKSLCDAYRKMCDEDPHLFAYNFREELKQGDGK
          ..LADVDPTLRPT.QLSVLHFKSLCDAYRKMCDEDPH.FAYNFREELKQ...K
Retrocopy FRLADVDPTLRPT<QLSVLHFKSLCDAYRKMCDEDPHHFAYNFREELKQKSEK

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_963 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_963 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005709	1 retrocopy	retro_etel_734,
Macropus eugenii	ENSMEUG00000001699	1 retrocopy	retro_meug_1770,
Tursiops truncatus	ENSTTRG00000006327	1 retrocopy	retro_ttru_963 ,