RetrogeneDB ID: retro_ttru_1286

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_109708:373382..373964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TVP23A
• Ensembl ID: ENSTTRG00000015641
• Aliases: None
• Description: trans-golgi network vesicle protein 23 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:20398]

Sequence

>retro_ttru_1286
GCCGCCATGTTGCAGCAGGACAGTAATGATGACATTGAAGATGTTTCACTGTTTGATGCAGAAGAGGAGACAACTAGTAG
ACCAGAAAAATCCAAAATCAGTCACCCAGTGGCATCATTTCTCCATTTATTCTTTCGAGTCAGTGCAATTATAGTCTATG
TTCCCTGTGAATGGTTCAGCACCAGCTTTATTGCCTGTATGGTGACAGTTATCTTGTTGTTGTCATGTGACTTCTGGGCA
GTCAAGAATGTCACAGGTAGACTAATGGTTGGCCTGCACTGGTGGAATCACACTGATGAAGATGGAAAAAGCCATTGGGT
GTCTGAGTCCAGGAAGGCCTTTCCTCAAGACAGTAAAACTGTTTCAGAGGCTGAATCAAGAATCTCCTGGTTAGGACTCA
TCGCCTGTCTGGTGCTGTGGGTAATATTTGCCTTTAGTGCCCTCTTCTCCTTCAGAGTGAAGTGACTAGCGGTGGTTATC
ATGGGTGTGGTGCTGCAAGGGGCCGACCTGTATGGCTACATCAGGTGCAAAGTGGGCAGCAGGAAGAATTTAACCAGCAT
GGCTACATCGTACCTCGGAAAG

Alignment

ORF - retro_ttru_1286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.92 %
• Parental protein coverage: 75.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGRMKQALVDDTEDVSLDFGNEEELAFR--KAKIRHPVATFFHLFFRVSATITYVGCDWFSRSFVGCFVT
          A....Q...DD.EDVSL.F..EEE...R..K.KI.HPVA.F.HLFFRVSA.I.YV.C.WFS.SF..C.VT
Retrocopy AAMLQQDSNDDIEDVSL-FDAEEETTSRPEKSKISHPVASFLHLFFRVSAIIVYVPCEWFSTSFIACMVT

Parental  VLLLLSFDFWSVKNVTGRLLVGLRWWNQIDEDGKSHWIFEARKVSP-NTVAATEAEARVFWLGLIICPMI
          V.LLLS.DFW.VKNVTGRL.VGL.WWN..DEDGKSHW..E.RK..P.......EAE.R..WLGLI.C...
Retrocopy VILLLSCDFWAVKNVTGRLMVGLHWWNHTDEDGKSHWVSESRKAFPQDSKTVSEAESRISWLGLIACLVL

Parental  WIVFFFSSLFSLKLKWLALVIVGISLQAANLYGYVLCKMGGESDISKVTASFLSQ
          W..F.FS.LFS...K.LA.VI.G..LQ.A.LYGY..CK.G..........S.L..
Retrocopy WVIFAFSALFSFRVK*LAVVIMGVVLQGADLYGYIRCKVGSRKNLTSMATSYLGK

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_1286 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1286 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015782	2 retrocopies	retro_dord_528, retro_dord_565,
Nomascus leucogenys	ENSNLEG00000010137	1 retrocopy	retro_nleu_2447,
Pongo abelii	ENSPPYG00000007094	1 retrocopy	retro_pabe_1344,
Tursiops truncatus	ENSTTRG00000015641	1 retrocopy	retro_ttru_1286 ,