RetrogeneDB ID: retro_ttru_563

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2692:303798..304490(+)
• 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_563
CCCCCCACCACTGGGACTGGCGTGCCGGAGAGGAAGTCCTCTCCCCACCAAGCGTCTCCACCCAAGCCGAGGACACTGCG
CAGTGGGTGGGAAGCTAGTGCTGTGCCGAGGCCTGAGCCCCTGGCTGGCGTCGACCGCCCTCTGCACCGTGACCCAGGCA
CCGTGAAGAAGGTTCTCCCTCCGGAGGAGACGGAGCAGGTTTCCGTCAAGCCTGGCACAAAGACGTCTCTGACGACGGTG
GTGAAGAAGATCTCCTACCTGATGATGATGATGCAAGGCATGTCCCACGTGCTGGCCCACCCGCTGCGTGTCATCTCAGT
GCACTGCGTGGTCCAGTTCATGGGAGGAAGGCCAAGTACAGCGGAAAGTTGAGCTCCATTGGGAAGATTTTCACAGAAGA
GGGGCTGCTGGGATTCTTTGTCGGCTTGATCCCTCACCTCCTGGAAGGTGTGGTTTCCTTGCGGGGCTGTAACCTGCTGG
CCCGCTTCCTCAGTGCCTACCTGGTGGGTGACACTCCAGGGGGGCTGGAGAACGACCAGAATCCAGGTTCCCAGTTCAGC
CAGGCCCTAGCCATCCAGAGCCACCCCAGATATGTGATGGGGATGGCAGTGAGCGTACTGACCTACCCCTTCCTGCTGGT
GGGCGGTCTCATGGCTGTGAACACCTGCAGGCTGGGCCGCCGCCTCACTCCT

Alignment

ORF - retro_ttru_563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.83 %
• Parental protein coverage: 60.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PPTIGTNV-LGRKVLYLPSFFTYAKYIVQ-VDGKIGLFRGLSPRLMSNALSTVTR-GSMKKVFPPDEIEQ
          PPT.GT.V..G..VL..PS..T.A....Q.V.GK..L.RGLSP.L.S.AL.TVT..G..KKV.PP.E.EQ
Retrocopy PPTTGTGV<AGEEVLSPPSVSTQAEDTAQ<VGGKLVLCRGLSPWLASTALCTVTQ<GTVKKVLPPEETEQ

Parental  VANKDDMKTSLKKVVKETSY-EMMMQCVSRMLAHPLHVISMRCMVQFVG-REAKYSGVLSSIGKIFKEEG
          V..K...KTSL..VVK..SY..MMMQ..S..LAHPL.VIS..C.VQF.G.R.AKYSG.LSSIGKIF.EEG
Retrocopy VSVKPGTKTSLTTVVKKISYLMMMMQGMSHVLAHPLRVISVHCVVQFMG<RKAKYSGKLSSIGKIFTEEG

Parental  LLGFFVGLIPHLLGDVVFLWGCNLLAHFINAYLVDDSVSDTPGGLGNDQNPGSQFSQALAIRSYTKFVMG
          LLGFFVGLIPHLL..VV.L.GCNLLA.F..AYL....V.DTPGGL.NDQNPGSQFSQALAI.S....VMG
Retrocopy LLGFFVGLIPHLLEGVVSLRGCNLLARFLSAYL----VGDTPGGLENDQNPGSQFSQALAIQSHPRYVMG

Parental  IAVSMLTYPFLLVGDLMAVNNCGLQAGLPP
          .AVS.LTYPFLLVG.LMAVN.C.L...L.P
Retrocopy MAVSVLTYPFLLVGGLMAVNTCRLGRRLTP

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_563 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_563 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,