RetrogeneDB ID: retro_ttru_1283

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_109590:50918..51400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRPT1
• Ensembl ID: ENSTTRG00000010252
• Aliases: None
• Description: tRNA phosphotransferase 1 [Source:HGNC Symbol;Acc:20316]

Sequence

>retro_ttru_1283
ATGAACTTCTCTGGAGGAAAGAGGCAAGAAGCAGCAGGGCCCAGGGACAGACAGGCTCACAGACCCCAGGAACCAGACCA
AGATGTGCAAGTACCCAAAACTTGGTCCTATGACCTGTCATGGAGCCCTGGAGCTGGGGCTTCCCGTGGGGGTCAAAGCC
TTCCTGCCCCTGGGCACCCTCCTACAGCTGCCCCAGTCCCACAGCTTCTCAGCTGAAGATGTGCAGCAAGTGGTGAACAC
CATGGGGAAGCAGTGGTTCACACTGCAGCCAGGGGACCCCGGCATTGGCTCTCATCCAAGCCAATCTTGGTCACTTCCTG
CAAGTACCTGAGATGGATCTGATGCCCTTGGCAACCCGACAGGCCCTGCCCCTGATGCTTATTTATAGCACATTCTGGCA
GCACTGGCCATCCATCCCGTTCAAAAGCATGTCCTGCTGGGGAAGGAGGCACATCCACCTGGCCTCAGGACTGCCTGGGG
AC

Alignment

ORF - retro_ttru_1283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.98 %
• Parental protein coverage: 64.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNAPRGRRQEAAGPKGRRAQR-PREQDRDVQLSKALSYALRHGALKLGLPMGPDGFVPLDTLLQLPQFCS
          MN...G.RQEAAGP..R.A.R.PR.Q.......K.L.....HGAL.LGLP.G...F.PL.TLLQLPQ..S
Retrocopy MNFSGGKRQEAAGPRDRQAHR>PRNQTKMCKYPK-LGPMTCHGALELGLPVGVKAFLPLGTLLQLPQSHS

Parental  FSVEDVQRVVDTNGKQRFALQP-GDPGAGPLIRANQGHSLKVPELELIPLETPQALPLVLVHGTFWQHWP
          FS.EDVQ.VV.T.GKQ.F.LQP.G.P....LI.AN.GH.L.VPE..L.PL.T.QALPL.L...TFWQHWP
Retrocopy FSAEDVQQVVNTMGKQWFTLQP>GTPALA-LIQANLGHFLQVPEMDLMPLATRQALPLMLIYSTFWQHWP

Parental  SILLKGLSCWGRTHIHLAAGLLGD
          SI..K..SCWGR.HIHLA.GL.GD
Retrocopy SIPFKSMSCWGRRHIHLASGLPGD

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_1283 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1283 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
Equus caballus	ENSECAG00000009917	1 retrocopy	retro_ecab_1055,
Sus scrofa	ENSSSCG00000013040	1 retrocopy	retro_sscr_1146,
Tursiops truncatus	ENSTTRG00000010252	1 retrocopy	retro_ttru_1283 ,