RetrogeneDB ID: retro_ttru_1239

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_108325:18170..18906(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDEL1
• Ensembl ID: ENSTTRG00000006517
• Aliases: None
• Description: nudE nuclear distribution E homolog (A. nidulans)-like 1 [Source:HGNC Symbol;Acc:17620]

Sequence

>retro_ttru_1239
AGACTGAAGTATGAAGTGGAAGCACTAACGGAGAACCTGGAGCATCAACATGCACAGAGCTACAAGCAGGTCTCAGTATT
AGAAGAAGATTTAAGTCAGACTCGGGCCTTTAAGCAGCAGTTACATAAGTATGTGAGAGAGCTGGAGCCGGCCGGTGATG
ACCTGGAGTGAGCAAAAAGGGCAACAGTAGTTTCACTGGAAGACTTTGAACAAGGCTAAATCAAGCCATTGAACGAAATG
CATTTTTAAAAAGTGAACTTGATGAAAAGGAATCTTTGTTGGTCTCTGTACAGAGGTTAATGGATGAAGCGAGAGATTTA
AGACAACAGCTAGCTGTTGGGGAAAGACAACAGGAAGTAACTAGAAAGTTGGCTCCCAGTTCTCCAACTCTAGACTGGGA
AAAGATGGATTCTGCCGTCCAAGCATCACTTTCTTTGCCAGCTACTCCTGTTGGCAACGGAACAGAGAACAGTTTTCCTT
CACTGAAATCTATACCAAACGGTTTTGGTACCGGTCCACTGACTCCTTCAGCTAGGATATCAGCACCAAACATCGTGTGG
GATCGCTGACGGAAAGTAGGGGTTTTAGAATCCAAATTAGCAGCTGGCAGGAAGTTTGCAAAGGCCCAAGCATCACGAAA
ATCTGTATTTCAGGGAACATTAACTGCGGGATGATGAATAGCCATGGCACGAAGTTCTCTCTATCAGGGCACTCGTCTTT
CTTCAACAAAGGGGCG

Alignment

ORF - retro_ttru_1239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.68 %
• Parental protein coverage: 67.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIVSLEDFE
          RLKYEVEAL.E.LEHQ.AQSYKQVSVLE.DLSQTRA.K.QLHKYVRELE.A.DDLE.AKRAT.VSLEDFE
Retrocopy RLKYEVEALTENLEHQHAQSYKQVSVLEEDLSQTRAFKQQLHKYVRELEPAGDDLE*AKRATVVSLEDFE

Parental  Q-RLNQAIERNAFLESELDEKESLLVSVQRLKDEARDLRQELAVRERQQEVTRKSAPSSPTLDCEKMDSA
          Q.RLNQAIERNAFL.SELDEKESLLVSVQRL.DEARDLRQ.LAV.ERQQEVTRK.APSSPTLD.EKMDSA
Retrocopy Q<RLNQAIERNAFLKSELDEKESLLVSVQRLMDEARDLRQQLAVGERQQEVTRKLAPSSPTLDWEKMDSA

Parental  VQASLSLPATPVGKGTENSFPSPKAIPNGFGTSPLTPSARISALNIVGDLLRKVGALESKLAACRNFAKD
          VQASLSLPATPVG.GTENSFPS.K.IPNGFGT.PLTPSARISA.NIV.D..RKVG.LESKLAA.R.FAK.
Retrocopy VQASLSLPATPVGNGTENSFPSLKSIPNGFGTGPLTPSARISAPNIVWDR*RKVGVLESKLAAGRKFAKA

Parental  QASRKSY-ISGNVNCGVMNSNGTKFSRSGHTSFFDKGS
          QASRKS..ISGN.NCG.MNS.GTKFS.SGH.SFF.KG.
Retrocopy QASRKSV<ISGNINCGMMNSHGTKFSLSGHSSFFNKGA

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_1239 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1239 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014341	1 retrocopy	retro_cjac_4072,
Cavia porcellus	ENSCPOG00000012878	1 retrocopy	retro_cpor_626,
Pan troglodytes	ENSPTRG00000008744	1 retrocopy	retro_ptro_2000,
Ictidomys tridecemlineatus	ENSSTOG00000027930	1 retrocopy	retro_itri_620,
Tursiops truncatus	ENSTTRG00000006517	1 retrocopy	retro_ttru_1239 ,