RetrogeneDB ID: retro_ttru_1101

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_103053:52689..53324(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH1
• Ensembl ID: ENSTTRG00000001966
• Aliases: None
• Description: mitochondrial carrier 1 [Source:HGNC Symbol;Acc:17586]

Sequence

>retro_ttru_1101
GACCAAGACCCCCACCACCAAGCTCTTTTCATGGTGCTGGGCGCAGGGGTGACAGAGCTCAGTCACCAGCTGCTCTACAT
GGAGCTGCCCATCAGACGGGTCATGAGCCAATACCCACACCATTGAGACCAATGGGCTGGGGAGGAAGGGTCCTCCACCC
TCCGACCCTTCTTCACCTATGCCCAAAGGACATTGTGCAAGTGGATGGGAAGATAGGCTGTTCCGAGGCCTGAGCTGCTG
GCTGACGTCCACTGCCCTCTCCACCATGACCCCGGGCAGCATGAAGAAGATTTTCTCTCCGGATGATATCGAGCAGGTTT
CCAGCAAGGATGACACGAAGATTTCTCTGAAGACTGTGGGGAAGGAGACCTCCTACCTGATGATGATGCAGGGAATGTCC
CACATATTGGCTCACCCCTTACGTGTCATCTCAATAGCTGCACGGTCCATTTTGTGGGACTGGAGACCAAGTACACTGGA
GAGTTGAGCTCCATTGGGAAGATTTTCAAAGATGAGGAGCTGCTGGGACTCTTTGTCAGCTAAATCCCTCACATCCTGGA
AGATGCGGTTTTCTTGCAGGGCTGTAACCTGCTGGCCACTTCCTCAGTGCCTACCTGGTGGATGACAGCTTCAGC

Alignment

ORF - retro_ttru_1101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.21 %
• Parental protein coverage: 54.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DNAPTTEALFVALGAGVTALSHPLLYVKLLI-QVGHEPMPP-TIGTNVLGRK-VLYLPSFFTYA-KYIVQ
          D..P...ALF..LGAGVT.LSH.LLY..L.I.Q.GHEP.P..TI.TN.LGRK.VL..P.......K.IVQ
Retrocopy DQDPHHQALFMVLGAGVTELSHQLLYMELPI<QTGHEPIPT<TIETNGLGRK>VLHPPTLLHLCPKDIVQ

Parental  VDGKIG-LFRGLSPRLMSNALSTVTRGSMKKVFPPDEIEQVANKDDMKTSLKKVVKETSYEMMMQCVSRM
          VDGKIG.LFRGLS..L.S.ALST.T.GSMKK.F.PD.IEQV..KDD.K.SLK.V.KETSY.MMMQ..S..
Retrocopy VDGKIG<LFRGLSCWLTSTALSTMTPGSMKKIFSPDDIEQVSSKDDTKISLKTVGKETSYLMMMQGMSHI

Parental  LAHPLHVISM-RCMVQFVGREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLA-HFIN
          LAHPL.VIS...C.V.FVG.E.KY.G.LSSIGKIFK.E.LLG.FV..IPH.L.D.VFL.GCNLLA.HF..
Retrocopy LAHPLRVISI<SCTVHFVGLETKYTGELSSIGKIFKDEELLGLFVS*IPHILEDAVFLQGCNLLA<HFLS

Parental  AYLVDDSVS
          AYLVDDS.S
Retrocopy AYLVDDSFS

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_1101 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1101 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137409	2 retrocopies	retro_hsap_3671, retro_hsap_856,
Gorilla gorilla	ENSGGOG00000003908	1 retrocopy	retro_ggor_2481,
Macaca mulatta	ENSMMUG00000021976	1 retrocopy	retro_mmul_1060,
Nomascus leucogenys	ENSNLEG00000010899	1 retrocopy	retro_nleu_423,
Pongo abelii	ENSPPYG00000016557	2 retrocopies	retro_pabe_3011, retro_pabe_691,
Pan troglodytes	ENSPTRG00000018115	1 retrocopy	retro_ptro_2490,
Tarsius syrichta	ENSTSYG00000014777	1 retrocopy	retro_tsyr_488,
Tursiops truncatus	ENSTTRG00000001966	2 retrocopies	retro_ttru_1101 , retro_ttru_563,
Tursiops truncatus	ENSTTRG00000014169	2 retrocopies	retro_ttru_1476, retro_ttru_353,