RetrogeneDB ID: retro_ttru_473

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2400:248309..249175(+)
• Located in intron of: ENSTTRG00000011500

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTX2
• Ensembl ID: ENSTTRG00000004650
• Aliases: None
• Description: orthodenticle homeobox 2 [Source:HGNC Symbol;Acc:8522]

Sequence

>retro_ttru_473
ATGTCTTATCTTAAGCAACCGCCTTACGCAGTCAGTGGGCTGAGTCTGACCACGTCGGACATGGGCTTGCTGCACCCCTT
GATGGGCTACCCGGCCACCCCTTGGGAACAGCGGCGGGAGAGGACGACGTTCACCCGGGCGCAGCTAGATGTGCTGGAAG
CGTTGTTGGCTAAGACCCGATACCCAGATGTCTTCATGTGGGAGGAGGTGGCACTGAAAATCAACTTGCCCGAGTCCAGG
GTACAGGTGTGGTTGAAGAACTGAAGCGCTAGGTGCCGCCGCCAGCAGCAGCAGCAGCAGCAGCAGAATGGAGGTCAAAA
CAGTGAGGCCTGCCAGAGAGAGGACGTCTCCTCTCGGGAAGTGAGCTCAGAGGGTGGAACAAGTGGCCAGTTCACTGCCC
CCTCTAGCACCTCAGGCCCAGCCGTTTCCAGCAGCAGTGCTCCTGTGTCTATCTGGAGCCCAGCTTCCGTCCCCCCACTG
TCAGATCCCTCGTCCACCTCCTCTTCCCGCATGCAGAGGTCCTGTCCCACGACCTATACTCAGGCTTCAGGTTACAGTCG
AGGATGTGCTGGCTCAACTTCCTGCTCTGGGGGCGTGGACTGTGGATCTCATGTGACCCCTATGCATCACCAGCTTCCCG
TGGAGGGACCACACTCAGTCCCACGGGCACCAGTGCAGTCCACCAGCCGTCTCAATCCGTCCCCAGCTTCTCTTTCCACC
CAGGGATATGGAGCTTCAAGCTTGGGTTTTAACTGAACCACCGACTGCTTGGATTATAAGGACCAAACTGCCTCCTGGAA
GCTTAACTTCAATGCTGACTGCTTGGATTATAAAGATAGACATCTTCGTGGGAATTCCAGGTTTTG

Alignment

ORF - retro_ttru_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.05 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSYLKQPPYAVNGLSLTTSGMDLLHPSVGYPATPRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREEV
          MSYLKQPPYAV.GLSLTTS.M.LLHP..GYPATP..QRRERTTFTRAQLDVLEAL.AKTRYPD.FM.EEV
Retrocopy MSYLKQPPYAVSGLSLTTSDMGLLHPLMGYPATPWEQRRERTTFTRAQLDVLEALLAKTRYPDVFMWEEV

Parental  ALKINLPESRVQVWFKNRRAKCRQ-QQQQQQNGGQNKVRPAKKKTSPAREVSSESGTSGQFTPPSSTSVP
          ALKINLPESRVQVW.KN..A.CR..........G..............REVSSE.GTSGQFT.PSSTS.P
Retrocopy ALKINLPESRVQVWLKN*SARCRRXXXXXXXXNGGQNSEACQREDVSSREVSSEGGTSGQFTAPSSTSGP

Parental  AISSSSAPVSIWSPASISPLSDPLSTSSSCMQRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTPMHH
          A.SSSSAPVSIWSPAS..PLSDP.STSSS.MQRS.P.TYTQASGYS.G.AGSTS..GG.DCGS..TPMHH
Retrocopy AVSSSSAPVSIWSPASVPPLSDPSSTSSSRMQRSCPTTYTQASGYSRGCAGSTSCSGGVDCGSHVTPMHH

Parental  QLP-GPGTTLSPMGTNAV-TSHLNQSPASLSTQGYGASSLGFNSTTDCLDYKDQTASWKLNFNADCLDYK
          QLP...GTTLSP.GT.AV.TS.LN.SPASLSTQGYGASSLGFN.TTDCLDYKDQTASWKLNFNADCLDYK
Retrocopy QLP<RGGTTLSPTGTSAV>TSRLNPSPASLSTQGYGASSLGFN*TTDCLDYKDQTASWKLNFNADCLDYK

Parental  DQ-TSSWKFQVL
          D..TSSW.FQVL
Retrocopy DR<TSSWEFQVL

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_473 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_473 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014741	1 retrocopy	retro_btau_687,
Callithrix jacchus	ENSCJAG00000018583	1 retrocopy	retro_cjac_1380,
Cavia porcellus	ENSCPOG00000003420	1 retrocopy	retro_cpor_149,
Sus scrofa	ENSSSCG00000005063	1 retrocopy	retro_sscr_417,
Tursiops truncatus	ENSTTRG00000004650	1 retrocopy	retro_ttru_473 ,