RetrogeneDB ID: retro_ttru_243

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1677:25929..26364(-)
• 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_243
TCCACTGAGGAGAAGATGGAGGCCGATTCCCGTTCCATCTATGTTGGCAATGTGGACTATGGTGCAACAGCAGAAGAGCT
GGAAGCACACTTTCATGGCTGTGGTTCAGTCAACTGTGTTACTATACTATGTGACAAATTTAGTGGCCATCCCAAAGGGT
TTGCATATATAGAGTTCTCAGACAAAGAGTCAGTGAGGACTTCCTTGGCCTTAGATGAGTCCCTATTTAGAGGAAGACAA
ATCAAGGTGATCCCAAAACAAACCAACAGACCAGGCATCAGCACAACAGACTGGGGTTTCCCGCGAGCCTGATACCGTGC
CCGGACCACCAACTACAACAGTTCCCACTCTCTATTCTACAGTGGTTTTAACAACAGGCCCTGGGGTCATGTCTACAGGG
GCCGGGCTAGAGCGACATCATAGTATTCCCCTTAC

Alignment

ORF - retro_ttru_243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.24 %
• Parental protein coverage: 51.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPTEALEADHRSVYVGNVDYGGTAQELEAYFNHCGEIQRVTILCDKFSGHPKGYAYIEFATESSAQAAVE
          S..E..EAD.RS.YVGNVDYG.TA.ELEA.F..CG....VTILCDKFSGHPKG.AYIEF....S......
Retrocopy STEEKMEADSRSIYVGNVDYGATAEELEAHFHGCGSVNCVTILCDKFSGHPKGFAYIEFSDKESVRTSLA

Parental  LDKSVFRGRVIKVLPKRTNLPGISSTDRGGLRGHPGARGGPF--PHSNFQGGARFRPRGR-NRGRGRFSP
          LD.S.FRGR.IKV.PK.TN.PGIS.TD.G..R....AR.......HS.F..G...RP.G...RGR.R...
Retrocopy LDESLFRGRQIKVIPKQTNRPGISTTDWGFPRA*YRARTTNYNSSHSLFYSGFNNRPWGHVYRGRARATS

Parental  WYSPY
          .YSPY
Retrocopy *YSPY

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_243 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_243 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.

---

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,