RetrogeneDB ID: retro_ttru_1040

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_100723:123832..124854(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC3
• Ensembl ID: ENSTTRG00000009239
• Aliases: None
• Description: 5'-nucleotidase domain containing 3 [Source:HGNC Symbol;Acc:30826]

Sequence

>retro_ttru_1040
CACCATGACATCACGTCCCTGTTCATGGACATCTTCTCCCTGCCCGAGATGACCCTGCTGTCCTGTGTGAACGAGTACTT
TCTGAAGAACAACATCGACTATGAGCCTGTGCACCTGTACAAAGACGTCAAGGATTCAATTCGGGAGGTGCACACCAAAG
GAATCATGTACAGAGCAGTTGAAGCAATATTGAAAAGTACATCTGCTACCCTGAGCAGACCCATGCAGTGTTGGCCAAAC
TGGCTGATCATGGCAAGAAGATGTTTCTCATCACCAATAGCCCCAGTAGCTTTGTGGATGAAGGGATGAGGTATATTGTT
GAAAAAGACTGGAGGGACCTGTTTGATGTGGTCATCGTTCAGGCAGAGAAGCCAAACTTCTTTAGTGATAAGTGGAGTCC
CTTCCAAAAGGTGAATGTGAAAGGCGTCTTACTCTAGGATAAAATCTACACGTTGCAGAAAGGCCAGATTTATAAGCAGG
GCAATTTAGATGAACTTTTGAAGTTTACTGGATGGTGGGGATCCAAAGTGTTGTATTTTGGTGACCATGTATACAGTGAC
CTGGTGGACTTGACCCTAAAGCATGGCTGGTGAACGGGTGCAATTATCCTGGAATTGAGATCTGAGCTCAGAATCATGAA
CATGGAAAAGTACATTCAAACAATTACCTGGCTACAGACCTTGACTGGGTTATTGGAGCAGATGCAGGTTCACAGAGATG
CGGAGTCACAGCTGGTTTTGCAGGAGTGCAAAAAGGAGAGGAAGGAGTTGAGAGAAATGACCAAATGTTCCTTCAGCGCC
CAGTTTGGAAGCTTGTTCCGCATAGACCAGAACCCCACGTACTTCCTGCGGCGCCTGTTGCGATTTGCCGACATCTACGT
GGCATCCCTGAGCTGCCTCCTGAGCTATGACATCAGCTACACGTTCTACCCCTGGAGGACCCCACTGCAGCACAAGCTTC
CTGCCTGGTCCGACAGGCCCCCGGCCGCCAGGCTGCCACTCCTGCAGGAGGCCCAGGCCAAG

Alignment

ORF - retro_ttru_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 81.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HGNTMKQFMDIFSLPEMTLLSCVNEYFLKNNIDYEPVHLYKDVKDSIRDVHTKGIMYRAIEA-DIEKYIC
          H......FMDIFSLPEMTLLSCVNEYFLKNNIDYEPVHLYKDVKDSIR.VHTKGIMYRA.EA..IEKYIC
Retrocopy HHDITSLFMDIFSLPEMTLLSCVNEYFLKNNIDYEPVHLYKDVKDSIREVHTKGIMYRAVEA<NIEKYIC

Parental  YPEQTRAVLAKLADHGKKMFLITNSPSSFVDKGMRYIVGKDWRDLFDVVIVQAEKPNFFNDKRRPFRKVN
          YPEQT.AVLAKLADHGKKMFLITNSPSSFVD.GMRYIV.KDWRDLFDVVIVQAEKPNFF.DK..PF.KVN
Retrocopy YPEQTHAVLAKLADHGKKMFLITNSPSSFVDEGMRYIVEKDWRDLFDVVIVQAEKPNFFSDKWSPFQKVN

Parental  EKGVLLWDKIYKLQKGQIYKQGNLYEFLKLTGWRGSKVLYFGDHIYSDLADLTLKHGWRTGAIIPELRSE
          .KGVLL.DKIY.LQKGQIYKQGNL.E.LK.TGW.GSKVLYFGDH.YSDL.DLTLKHGW.TGAII.ELRSE
Retrocopy VKGVLL*DKIYTLQKGQIYKQGNLDELLKFTGWWGSKVLYFGDHVYSDLVDLTLKHGW*TGAIILELRSE

Parental  LRIMNTEQYIQTMTWLQTLTGLLEQMQVHRDAESQLVLQEWKKERKEMREMTKGSFNTQFGSLFRTDQNP
          LRIMN.E.YIQT.TWLQTLTGLLEQMQVHRDAESQLVLQE.KKERKE.REMTK.SF..QFGSLFR.DQNP
Retrocopy LRIMNMEKYIQTITWLQTLTGLLEQMQVHRDAESQLVLQECKKERKELREMTKCSFSAQFGSLFRIDQNP

Parental  TYFLRRLSRFADIYMASLSCLLSYDVSHTFYPRRTPLQHELPAWSDRSPATRPPLLQEAQAK
          TYFLRRL.RFADIY.ASLSCLLSYD.S.TFYP.RTPLQH.LPAWSDR.PA.R.PLLQEAQAK
Retrocopy TYFLRRLLRFADIYVASLSCLLSYDISYTFYPWRTPLQHKLPAWSDRPPAARLPLLQEAQAK

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_1040 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1040 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000006350	1 retrocopy	retro_mmul_915,
Tursiops truncatus	ENSTTRG00000008562	1 retrocopy	retro_ttru_1120,
Tursiops truncatus	ENSTTRG00000009239	1 retrocopy	retro_ttru_1040 ,