RetrogeneDB ID: retro_ttru_1205

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_107127:196539..197386(+)
• Located in intron of: ENSTTRG00000004260

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDI1
• Ensembl ID: ENSTTRG00000011454
• Aliases: None
• Description: GDP dissociation inhibitor 1 [Source:HGNC Symbol;Acc:4226]

Sequence

>retro_ttru_1205
GAATGTATCCTGTCAGGTATAATGTCAGTGAATGGAAAGAAAGTTCTTCACATGGATACAAACCCATATTAGGGAGGAGA
GAGTGCATCATCTGTAACACCACTGGAAGATTTATACAAAAGATTTAAAATACCTGGAGCACCACCGGCATCAATGGGGA
GAGGAAGAGACTGGAATGTTGACTTCATTCCCAAGTTCCTTATGGCAAATGGTCAGCTGGTTAAGATGCTGCTTTTTACA
CAGGTCATTCGCTATCTGGATTTCCAAGTGACTGAAGGGAGCTTTGTTTGTAAAGGAGGAAAGATCTACAAGGCTCCTTC
CACTGAAGCAGAAGCTCTGGCATCTAGCCTAATGGGGCATTTGAAAAACGTCGATTCAGAAAATTCCTGGTGTATGTTGC
CAACTTTGATGGGAATGATCCTAGAACTTTTGAGGGCGTTGATCCTAGGAAGATGGCAATGAGAGAGGTGTATAAGAAAT
CTGACTTGGGCCAAGATGTCATAGGTTTTACTGGTCATGCGCTGGCACTTTACAGAACTGATGACTGTTTATATCAACCA
TGTGGTGAAACCATTAACAGGATTAAACTTTACAGTGAGTCTTTGGCAAGATATGGCAAAAGCCCATACCTTCATCCACT
CTACAGCCTTGGATAACTGCCACAGGATTTTCACAGCTAAGTGCTATTTACGGAGGTACATACGTGCTGAATAAATCAAT
TGAAGAAATCATTATGCAAAATGGAAAAGTGATTGGTGTAAAATCTGAAGGAGAGATTGCTCGTTGTAAGAAGCTCACCT
GTGATCCCAGCTACTCCATCATCTTTGATCGAATAGAGAAAGCGGGC

Alignment

ORF - retro_ttru_1205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.6 %
• Parental protein coverage: 64.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ECILSGIMSVNGKKVLHMDRNPYYGGES-SSITPLEELYKRFQLLEGPPETMGRGRDWNVDLIPKFLMAN
          ECILSGIMSVNGKKVLHMD.NPY.GGES.SS.TPLE.LYKRF.....PP..MGRGRDWNVD.IPKFLMAN
Retrocopy ECILSGIMSVNGKKVLHMDTNPY*GGESASSVTPLEDLYKRFKIPGAPPASMGRGRDWNVDFIPKFLMAN

Parental  GQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVPSTETEALASNLMG-MFEKRRFRKFLVFVANFDEN
          GQLVKMLL.T.V.RYLDF.V.EGSFV.KGGKIYK.PSTE.EALAS.LMG..FEKRRFRKFLV.VANFD.N
Retrocopy GQLVKMLLFTQVIRYLDFQVTEGSFVCKGGKIYKAPSTEAEALASSLMG<AFEKRRFRKFLVYVANFDGN

Parental  DAKTFEGVDPQNTSMRDVYRKFDLGQDVIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLARYGKSP
          D..TFEGVDP....MR.VY.K.DLGQDVI.FTGHALALYRTDD.L.QPC.ETINRIKLYSESLARYGKSP
Retrocopy DPRTFEGVDPRKMAMREVYKKSDLGQDVIGFTGHALALYRTDDCLYQPCGETINRIKLYSESLARYGKSP

Parental  YLYPLYGLGELPQ-GFARLSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPSY--VPDR
          YL.PLY.LG.LPQ.GF..LSAIYGGTY.LNK....IIM.NGKV.GVKSEGE.ARCK.L.CDPSY....DR
Retrocopy YLHPLYSLG*LPQ<GFSQLSAIYGGTYVLNKSIEEIIMQNGKVIGVKSEGEIARCKKLTCDPSYSIIFDR

Parental  VRKAG
          ..KAG
Retrocopy IEKAG

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_1205 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1205 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000010921	4 retrocopies	retro_meug_1228, retro_meug_2135, retro_meug_561, retro_meug_795,
Microcebus murinus	ENSMICG00000016418	1 retrocopy	retro_mmur_1095,
Sarcophilus harrisii	ENSSHAG00000005650	1 retrocopy	retro_shar_43,
Tupaia belangeri	ENSTBEG00000012540	4 retrocopies	retro_tbel_1832, retro_tbel_2262, retro_tbel_2457, retro_tbel_3930,
Tursiops truncatus	ENSTTRG00000011454	1 retrocopy	retro_ttru_1205 ,