RetrogeneDB ID: retro_ttru_412

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2176:253463..253886(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEX11A
• Ensembl ID: ENSTTRG00000015532
• Aliases: None
• Description: peroxisomal biogenesis factor 11 alpha [Source:HGNC Symbol;Acc:8852]

Sequence

>retro_ttru_412
ATGGACGCCTTTATCAGCTTCACCAACCAGACCCAGGGCCAGGACCAACTCTTCAGAGCCACTAAGTACACATGCATGTT
GCTTAGATATTTGTTAGAGCCTAAAGCTGACAAAGAGGAGGCTGTTATGAAGCTCAAGAAACTGGAGTCCAGTGTGAGCT
CTGGCCGTAAATGGTTCAGACTAGGCAATGTGGTACATGCTGTACAGGCGACTCAGCAGAGCATTCATGCCACTGACCTG
GTGCCCCGCGTATGCCTAACATTAGCCAGCCTGAACCTTGTGATTTATTTCATCTGTGACCCCATCATCTTCGTGAGGAG
TGCAGGGCTTGCCTCTGGCATTAACAAAGAGAAATGGTGAACGTGGGCTGCACGCCATTACTACTATTCTCTTCTGCTGA
GCCTGGTCAGGGATCTGTATGAA

Alignment

ORF - retro_ttru_412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.94 %
• Parental protein coverage: 57.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDAFIRFTNQTQGRDRLFRATQYTCMLLRYLLEPKADKEEVVMKLKKLESSVSTGRKWFRLGNVVHAVQM
          MDAFI.FTNQTQG.D.LFRAT.YTCMLLRYLLEPKADKEE.VMKLKKLESSVS.GRKWFRLGNVVHAVQ.
Retrocopy MDAFISFTNQTQGQDQLFRATKYTCMLLRYLLEPKADKEEAVMKLKKLESSVSSGRKWFRLGNVVHAVQA

Parental  IQQSSHATDLVPRICLILASLNRVIYFICDTILFVRSVGLASGINKEKWRMWAARHYYYSLLLSLVRDLY
          .QQS.HATDLVPR.CL.LASLN.VIYFICD.I.FVRS.GLASGINKEKW..WAARHYYYSLLLSLVRDLY
Retrocopy TQQSIHATDLVPRVCLTLASLNLVIYFICDPIIFVRSAGLASGINKEKW*TWAARHYYYSLLLSLVRDLY

Parental  E
          E
Retrocopy E

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_412 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_412 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	ENSBTAG00000006140	1 retrocopy	retro_btau_111,
Dasypus novemcinctus	ENSDNOG00000014344	1 retrocopy	retro_dnov_11,
Tupaia belangeri	ENSTBEG00000004185	1 retrocopy	retro_tbel_2910,
Tursiops truncatus	ENSTTRG00000015532	1 retrocopy	retro_ttru_412 ,