RetrogeneDB ID: retro_ttru_975

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_869:811633..812297(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2Q1
• Ensembl ID: ENSTTRG00000013998
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2Q family member 1 [Source:HGNC Symbol;Acc:15698]

Sequence

>retro_ttru_975
CTGAAGCTGCTCCAGTTCCTTCTCCCCCGCGGCCTCGAGCGCTTCCGCATTGCCAGCGCCTTCCTGGACCAGCTGAGATG
CGAGTTCCCGCTGGCTGAGGCCAGAGGGGCCGGGACGAGGGCCGCGCCCGGACTGCATCTCTCCTCACAGGGGTCGGTGC
CTGGGGATCCCGTCTGCATCCACTGCAACATCACGGAGTCATACCCAGCTGTGCCCCCCATCTGGTCAGCGGAGTCCAGT
GACGCTAACTTGGCTGCTCTCTTGGAGAGGCTGGTGGACATAAAGAAGGGGAATACTCTGCTGTTGCAGCATCTGAAGAG
GATCATCTCCGACCTGTGTAAACTCTGTAACCTCCCTCAGCATCCAGATGTGGAGATGCTGGATCAGCCCTTGCCAGAAG
AGCAGTGTACACAGGAAGATGTATCTTCGGAAGGTGAAGATGAAGAGATGCCTGAGGACACAGAAGACCTAGATCACTAT
GAAATAAATGAGAGAAGAAGCGCCAGCTGAGGGCAAGAAATCTGAAGATGACGGCATTGGAAAAGAAAACTTGGCCATAC
CAAAGAAAATTAAAAAGACCCAGAGGCAAGATTACTTAAATGGTGCGGTGTCTGGCTCGGCGCAGGCTACTGACCAGGTG
ATGAAGGAGCTCAGGGATATATAC

Alignment

ORF - retro_ttru_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 52.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKLLESIFHRGHERFRIASACLDELSCEFLLAGAGGAGAGAAPGPHLPPRGSVPGDPVRIHCNITESYPA
          LKLL.....RG.ERFRIASA.LD.L.CEF.LA.A.GAG..AAPG.HL...GSVPGDPV.IHCNITESYPA
Retrocopy LKLLQFLLPRGLERFRIASAFLDQLRCEFPLAEARGAGTRAAPGLHLSSQGSVPGDPVCIHCNITESYPA

Parental  VPPIWSVESDDPNLAAVLERLVDIKKGNTLLLQHLKRIISDLCKLYNLPQHPDVEMLDQPLPAEQCTQED
          VPPIWS.ES.D.NLAA.LERLVDIKKGNTLLLQHLKRIISDLCKL.NLPQHPDVEMLDQPLP.EQCTQED
Retrocopy VPPIWSAESSDANLAALLERLVDIKKGNTLLLQHLKRIISDLCKLCNLPQHPDVEMLDQPLPEEQCTQED

Parental  VSSEDEDEEMPEDTEDLDHYEMKE-EE-PAEGKKSEDDGIGKENLAILEKIKKNQRQDYLNGAVSGSVQA
          VSSE.EDEEMPEDTEDLDHYE..E.EE.PAEGKKSEDDGIGKENLAI..KIKK.QRQDYLNGAVSGS.QA
Retrocopy VSSEGEDEEMPEDTEDLDHYEINE>EEAPAEGKKSEDDGIGKENLAIPKKIKKTQRQDYLNGAVSGSAQA

Parental  TDRLMKELRDIY
          TD..MKELRDIY
Retrocopy TDQVMKELRDIY

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_975 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_975 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008889	1 retrocopy	retro_dnov_449,
Macropus eugenii	ENSMEUG00000003718	2 retrocopies	retro_meug_1816, retro_meug_358,
Microcebus murinus	ENSMICG00000001427	1 retrocopy	retro_mmur_339,
Rattus norvegicus	ENSRNOG00000020791	1 retrocopy	retro_rnor_297,
Tupaia belangeri	ENSTBEG00000013007	1 retrocopy	retro_tbel_3091,
Tursiops truncatus	ENSTTRG00000013998	1 retrocopy	retro_ttru_975 ,