RetrogeneDB ID: retro_ttru_185

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1513:17409..18102(+)
• Located in intron of: ENSTTRG00000011417

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX7
• Ensembl ID: ENSTTRG00000009853
• Aliases: None
• Description: syntaxin 7 [Source:HGNC Symbol;Acc:11442]

Sequence

>retro_ttru_185
GCTGCTCAGATAAAGAATTTGATGAGCCAACTAGGAACTAAGCAAGATTCAAGCAAGCTACAGGAAAATCTGCAACAGTT
ACAGCACTCTACAAATCAGCTTGCCAAGGAAACAAATGAATTACTGAAGGAATTAGGGTCCTTGCCCCTTCCTTCATCTA
CTTCAGAACAGCGCCAGCAGAAACTTCAGAAGGAACGTCTCATGAATGACTTCTCTGCAGCCTTAAACAATTTCCAGGCT
GTGCAGAGAAGGGTATCTGAAAAGGAAAAGGAGAGTATTGCCAGAGCAAGAGCTGGATCTCGTCTTTCTGTGGAGGAGAG
GCAAAGAGAGGAGCAACTCGTCTCATCTGACAGCCATGAGGAGTGGAACCAGATGCAGAGCCAGGAGGATGAGGTGGCCA
TCACTGAACAGGATTTGGAACTTATTAAAGACAGGGAAACGGCAATTCAGCAGCTGGAGGCTGATATTTTGGATGTCACT
CAGATATTTAAAGATTTGGCAATGATGATCCATGACCAAGGTGATCTCATTGACAGCATAGAAGCCAATGTGGAAAGCTC
AGAGGTGCATGTAGAAAGAGCCACTGATCAGTTACAGCGAGCTGCTTACTATCAGAAAAAATCTCACAATAAGATCTGTA
TCCTGGTGCTTGTCCTGTCAGTGATTATTGTAATCTTGGGACTTATTTTGTGG

Alignment

ORF - retro_ttru_185 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.27 %
• Parental protein coverage: 92.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAEIQRTLNQLGTPQDSPELRQQLQQKQQYTNQLAKETDKYIKEFGSLP--TTPSDQRQRKIQKDRLVAE
          .A.I.....QLGT.QDS..L...LQQ.Q..TNQLAKET....KE.GSLP.....S.QRQ.K.QK.RL...
Retrocopy AAQIKNLMSQLGTKQDSSKLQENLQQLQHSTNQLAKETNELLKELGSLPLPSSTSEQRQQKLQKERLMND

Parental  FTTSLTNFQKAQRQAAEREKEFVARVRASSRVSGGFPEESSKERNLVSWESQTQ-PQVQVQDEE--ITED
          F...L.NFQ..QR...E.EKE..AR.RA.SR.S....EE...E..LVS..S.....Q.Q.Q..E..ITE.
Retrocopy FSAALNNFQAVQRRVSEKEKESIARARAGSRLS---VEERQREEQLVSSDSHEEWNQMQSQEDEVAITEQ

Parental  DLRLIQERESSIRQLEADIMDINEIFKDLGMMIHEQGDVIDSIEANVENAEVHVQQANQQLSRAADYQRK
          DL.LI..RE..I.QLEADI.D...IFKDL.MMIH.QGD.IDSIEANVE..EVHV..A..QL.RAA.YQ.K
Retrocopy DLELIKDRETAIQQLEADILDVTQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRAAYYQKK

Parental  SRKTLCIIIFILVIGVVIIGLIIW
          S....CI....L....VI.GLI.W
Retrocopy SHNKICILVLVLSVIIVILGLILW

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_185 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_185 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010117	3 retrocopies	retro_chof_1503, retro_chof_2631, retro_chof_829,
Dasypus novemcinctus	ENSDNOG00000000295	1 retrocopy	retro_dnov_600,
Felis catus	ENSFCAG00000002292	1 retrocopy	retro_fcat_977,
Myotis lucifugus	ENSMLUG00000004301	1 retrocopy	retro_mluc_494,
Sarcophilus harrisii	ENSSHAG00000014440	1 retrocopy	retro_shar_430,
Tursiops truncatus	ENSTTRG00000009853	1 retrocopy	retro_ttru_185 ,