RetrogeneDB ID: retro_ttru_1833

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_93585:11341..12237(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NHEJ1
• Ensembl ID: ENSTTRG00000010020
• Aliases: None
• Description: nonhomologous end-joining factor 1 [Source:HGNC Symbol;Acc:25737]

Sequence

>retro_ttru_1833
ATGGAGGAACTGGAGCAAGGCCTGCAGATGCAGCCGTGGGCATGGCTACAGCTTGCCGAGAACTCCCTCTTGGCCAAGGC
TTATATCACTAAGCAGGGCTATGCCTTGTTGCTTTCAGATCTTCAACAGGTGTGGCCTGAACAGGTGGACACTAGTGTGA
TCAGCCAGCAAGCCAAGGAGCTGAACAAACACCTGACTGCTCCTCCTGAGGCTTTTCATTGTCATTTGTATGACCTGCTT
TGCCCATTGTTGAAGGACAGTGTTTGCCCTGGCAAAGCTACATTCTCCTGTGATCATGTGGCAGAGGTGCTGATACTCCA
GGTGTGGAGTGAGCTCTCTGGTCTCCCATTCTATTGGAATTTCCACTGCATCCTAGCTAACCCTTCACTGTTCTCCCAAC
ATTTGATTTGTCCTCTGATGGGCATGAGTCTGTCACTGCAGTGCCAAGTGAGGGACCTAGCAACATTGCTTTGTATGTAA
GATCTAGAGATCCAGGACTACCAGGACAGTGGGTCTATGCTGAGCCAAAATCAGTTGAAGACAGAGCCATTTGAAAAGAA
TTCCTTCTTGGAACAATTTATGGTAGAGAAAATACCAGAGGTATGCAGTGTTGGTGATGGAAAACCCTTTGTCACAAATC
TACAGAGTCTGTATATGGCAGTCACCAGACAAAAGATCCAAGTGGGACAGAAGCTTCAAGGCACTGGAGATCCCCAGACC
TCAAGCAGTGCCTCCTCACAAGGAACAGATAGCCAGCTTCTGAATCAGCCAGAAGAGCAGGTCTCCTCAGCACCATCCTT
CCCAGTGCCTGAAAAAGAGCCACAGTTACTTCAGGCCCTATGCAGAGACCTCAGTTGTTGAAGGTCAAGAGGTAGAAGCT
AGGGGGGCTCTTCAGT

Alignment

ORF - retro_ttru_1833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEELEQGLLMQPWAWLQLAENSLLAKAYITKQGYALLVSDLQQVWHEQVDTSVISQRAKELNKRLTAPPA
          MEELEQGL.MQPWAWLQLAENSLLAKAYITKQGYALL.SDLQQVW.EQVDTSVISQ.AKELNK.LTAPP.
Retrocopy MEELEQGLQMQPWAWLQLAENSLLAKAYITKQGYALLLSDLQQVWPEQVDTSVISQQAKELNKHLTAPPE

Parental  AFLCHLDDLLCPLLKDTACPGKATFSCDRVAEALILRVRSELSGLPFYWNFHCILASPSLVSQHLIRPLM
          AF.CHL.DLLCPLLKD..CPGKATFSCD.VAE.LIL.V.SELSGLPFYWNFHCILA.PSL.SQHLI.PLM
Retrocopy AFHCHLYDLLCPLLKDSVCPGKATFSCDHVAEVLILQVWSELSGLPFYWNFHCILANPSLFSQHLICPLM

Parental  GMSLALQCQVRDLATLLHMKDLEIQDYQESGATLSRDRLKTEPFEENSFLGQFMVEKLPEACSVGDGKRF
          GMSL.LQCQVRDLATLL.M.DLEIQDYQ.SG..LS...LKTEPFE.NSFL.QFMVEK.PE.CSVGDGK.F
Retrocopy GMSLSLQCQVRDLATLLCM*DLEIQDYQDSGSMLSQNQLKTEPFEKNSFLEQFMVEKIPEVCSVGDGKPF

Parental  VTNLQSLYMAVTRQEIQVGQKLRGTEDPQASSSASSQGTDSQLLNQPEEPDSSAPPLPVPEKEP-TVTSG
          VTNLQSLYMAVTRQ.IQVGQKL.GT.DPQ.SSSASSQGTDSQLLNQPEE..SSAP..PVPEKEP.TVTSG
Retrocopy VTNLQSLYMAVTRQKIQVGQKLQGTGDPQTSSSASSQGTDSQLLNQPEEQVSSAPSFPVPEKEP<TVTSG

Parental  PTQRPQLLKVKRKKLRGLFS
          P.QRPQLLKVKR.KL.GLFS
Retrocopy PMQRPQLLKVKR*KLGGLFS

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_1833 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1833 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031041	1 retrocopy	retro_btau_856,
Tursiops truncatus	ENSTTRG00000010020	1 retrocopy	retro_ttru_1833 ,