RetrogeneDB ID: retro_ttru_1488

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_114571:61254..61716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1L
• Ensembl ID: ENSTTRG00000004691
• Aliases: None
• Description: poly(A) binding protein, nuclear 1-like (cytoplasmic) [Source:HGNC Symbol;Acc:37237]

Sequence

>retro_ttru_1488
CCAGGCAGTGCTGGCCCAGTGATCATGTCCACTGAGGAGAAGCTGGAGGCTGATGCCCGTTCCATCTATGTTGACAATGT
GGACTATGGTGCAACAGCATAAGAGCTGGAAGCACACTTTTATGGCTGTGGTTCAGTCAACCGTGTTACTATACTATGTG
ACAAATTTAGTGGTCATCCCAAAGGGTTTGCATATATAGAGTTCTCAGACAAAGAGTCAGTGAGGACTTCCTTGGCCTTA
GATGAGTCCCTATTTAGAGGAAGACAAATCAAGGTGATCCCAAAACGAATGAACAGACCAGGCATCAGCACAACAGACCG
GGGTTTCCTGCGAGCCTGATACCGTGCCCGGACCACCAACTACAACAGTTCCCGCTCTCGATTCTACAGTGGTTTTAACA
GCAGGCCCCAGGGTCCTGTCTACAGGGGCTGGGCTAGAGCGACATCATGGTATTCCCCTTAC

Alignment

ORF - retro_ttru_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.49 %
• Parental protein coverage: 54.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PETGHPLSDSPTEALEADHRSVYVGNVDYGGTAQELEAYFNHCGEIQRVTILCDKFSGHPKGYAYIEFAT
          P....P...S..E.LEAD.RS.YV.NVDYG.TA.ELEA.F..CG...RVTILCDKFSGHPKG.AYIEF..
Retrocopy PGSAGPVIMSTEEKLEADARSIYVDNVDYGATA*ELEAHFYGCGSVNRVTILCDKFSGHPKGFAYIEFSD

Parental  ESSAQAAVELDKSVFRGRVIKVLPKRTNLPGISSTDRGGLRGHPGARGGPF--PHSNFQGGARFRPRGR-
          ..S......LD.S.FRGR.IKV.PKR.N.PGIS.TDRG.LR....AR........S.F..G...RP.G..
Retrocopy KESVRTSLALDESLFRGRQIKVIPKRMNRPGISTTDRGFLRA*YRARTTNYNSSRSRFYSGFNSRPQGPV

Parental  NRGRGRFSPWYSPY
          .RG..R...WYSPY
Retrocopy YRGWARATSWYSPY

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_1488 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1488 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023752	1 retrocopy	retro_btau_972,
Erinaceus europaeus	ENSEEUG00000004747	1 retrocopy	retro_eeur_633,
Ochotona princeps	ENSOPRG00000005597	2 retrocopies	retro_opri_1001, retro_opri_174,
Tursiops truncatus	ENSTTRG00000004691	3 retrocopies	retro_ttru_1488 , retro_ttru_243, retro_ttru_822,