RetrogeneDB ID: retro_ttru_899

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_545:130705..131613(-)
• Located in intron of: ENSTTRG00000003209

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX17
• Ensembl ID: ENSTTRG00000016920
• Aliases: None
• Description: syntaxin 17 [Source:HGNC Symbol;Acc:11432]

Sequence

>retro_ttru_899
ATGTCTGAAGATGAATAAAAAGTGAAATTTTTACGCCGTCTTGAACCAGCTCTTCAGAAATTTACTAAGATAGTAATCCC
AACAGACCTGGAGAGGTTAAGAAAGCACCAGCTAAATATTGAGAAGTATCAGAGGTGCAGAATCTGGGACAGGTTGCATG
AAGAGCATATCAATGCAGGACGTACCGTTCAGCAACTCCACTCCAGTATCCGAGAAATGGAGAAGCTTTGTTTGAAAGTC
CAAAGGGATGGCCTAGGACTTCTGAAGAGAATGATAGATCCTGTTAAAGAAGAAGCATCAGCAGCCACAGCAGAATTTCT
TCAACTCCATCTAGAATCTGTAGAAGAACTTAAGAAACAATTTAATGATGAAGAAACCTTATTACAGCCTTCTTTGACCA
GATCCATGGCTGTTGGTGGAACATTTCACGCTACTGAAGATGAAGCTAATACTCAGAGTATGACTCAGATATATGTGTTG
CCTGAAATTCCTCGAGATCAAAATGCTGCAGAATCATGGGAAACCTTAGAGGCGAACTCAATTGAACTTAGCCAACTGGT
CACTGATTTCTCTCTCCTAGTGAATTCTCAGCAGGAGAAGATTGACAGCGTTGAAGACCATATCAACAGTGCTGCTGTGA
GTGTTGAAGAGGGAACCAAAAACTTGGGGAAGGCTGCAAAGTACAAGCTGGCAGCTCTGCCTGTGGCAGGTGCTCTCATC
GGAGGAACGGTGGGGGCCCGACTGGCTTCCTTGCAGGCTTCAGAGTGGCAGGAATTGCAGCTGCGCTTGGTGGTGGGGTG
GTGGGCTTCACAGGTGGAAAATTGTTACAAAGAAAGAAACAGAAAGTGATGCAGAAGCTCACTTCCAGCTGTCCAAATCT
TTCCAGCCAAACTGACAAAAAATGCAGT

Alignment

ORF - retro_ttru_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSEDEEKVK-LRRLEPAIQKFTKIVIPTDLERLRKHQINIEKYQRCRIWDKLHEEHINAGRTVQQLRSNI
          MSEDE.KVK.LRRLEPA.QKFTKIVIPTDLERLRKHQ.NIEKYQRCRIWD.LHEEHINAGRTVQQL.S.I
Retrocopy MSEDE*KVKFLRRLEPALQKFTKIVIPTDLERLRKHQLNIEKYQRCRIWDRLHEEHINAGRTVQQLHSSI

Parental  REMEKLCLKVQKDDLGLLKRMIDPVKEEASAATAEFLQLHLESVEELM-QFNDE-TLLQPSLTRSMTVGG
          REMEKLCLKVQ.D.LGLLKRMIDPVKEEASAATAEFLQLHLESVEEL..QFNDE.TLLQPSLTRSM.VGG
Retrocopy REMEKLCLKVQRDGLGLLKRMIDPVKEEASAATAEFLQLHLESVEELKKQFNDEETLLQPSLTRSMAVGG

Parental  TFHTAEDEADPQSMTQIYVLPEIPRDQNAAESWETLEADLIELSQLVTDFSLLVNSQQEKIDSVEDHVNS
          TFH..EDEA..QSMTQIYVLPEIPRDQNAAESWETLEA..IELSQLVTDFSLLVNSQQEKIDSVEDH.NS
Retrocopy TFHATEDEANTQSMTQIYVLPEIPRDQNAAESWETLEANSIELSQLVTDFSLLVNSQQEKIDSVEDHINS

Parental  AAVNVEEGTKNLGKXXXYKLAALPVVGALIGGVV-GGPIGLLAGFKVAGIAAALGGGVLGFTGGKLLQRK
          AAV.VEEGTKNLGK...YKLAALPV.GALIGG.V.GGP.G.LAGF.VAGIAAALGGGV.GFTGGKLLQRK
Retrocopy AAVSVEEGTKNLGKAAKYKLAALPVAGALIGGTV<GGPTGFLAGFRVAGIAAALGGGVVGFTGGKLLQRK

Parental  KQKMMEKLTSSCPNLPSQTDKKCS
          KQK.M.KLTSSCPNL.SQTDKKCS
Retrocopy KQKVMQKLTSSCPNLSSQTDKKCS

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_899 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_899 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008016	1 retrocopy	retro_btau_1534,
Choloepus hoffmanni	ENSCHOG00000013030	1 retrocopy	retro_chof_131,
Myotis lucifugus	ENSMLUG00000011745	1 retrocopy	retro_mluc_760,
Tursiops truncatus	ENSTTRG00000016920	1 retrocopy	retro_ttru_899 ,