RetrogeneDB ID: retro_ttru_822

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3555:137372..137819(-)
• Located in intron of: ENSTTRG00000012730

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_822
CCACTGATCATGTCCATTGAGGAGAAGATGGAGGCCGATGCCCACTCCACCTACGTTGGCAAAGTGGACTGTGGTGCAGC
AGCGGAAGAGCTGGAAGCACACTTTCATGGCTGTGGTTCAGTCAACCACGTTACCATACTCTGTGACAAATTTAGTGGCC
ATCCCAAAGAGTTTGCTTATATAGAGTTCTCAGACAAACAGTCAGTGAGGGCTTCCCTGGCCTTAGATGACTCCCTATTT
AGAGGAAGACAAATCAAGGTGATCCCAAAGCGAACCAACAGACCAGGCATGAGCACAGCAGACCAGGGTTTCCCACAAGT
CCGATTCCGAGCCCGGACCCCCGACTACAACAGTTCCCCCTCTCAATTCTACAGTGGTTTTAACAGCAGGCCCTGGGGTC
ACGTCTACAGGGGCTGGGCTAAAGAGACATCATGGTATTCCCCTTAC

Alignment

ORF - retro_ttru_822 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.68 %
• Parental protein coverage: 52.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLSDSPTEALEADHRSVYVGNVDYGGTAQELEAYFNHCGEIQRVTILCDKFSGHPKGYAYIEFATESSAQ
          PL..S..E..EAD..S.YVG.VD.G..A.ELEA.F..CG....VTILCDKFSGHPK..AYIEF....S..
Retrocopy PLIMSIEEKMEADAHSTYVGKVDCGAAAEELEAHFHGCGSVNHVTILCDKFSGHPKEFAYIEFSDKQSVR

Parental  AAVELDKSVFRGRVIKVLPKRTNLPGISSTDRGGLRGHPGARGGPFPHSNFQ--GGARFRPRGR-NRGRG
          A...LD.S.FRGR.IKV.PKRTN.PG.S..D.G.......AR......S..Q...G...RP.G...RG..
Retrocopy ASLALDDSLFRGRQIKVIPKRTNRPGMSTADQGFPQVRFRARTPDYNSSPSQFYSGFNSRPWGHVYRGWA

Parental  RFSPWYSPY
          ....WYSPY
Retrocopy KETSWYSPY

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_822 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_822 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 ,