RetrogeneDB ID: retro_ttru_98

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1204:40057..40342(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC34
• Ensembl ID: ENSTTRG00000000391
• Aliases: None
• Description: cell division cycle 34 [Source:HGNC Symbol;Acc:1734]

Sequence

>retro_ttru_98
CCACGCCAGTCCATGACGCCCTCAGAGAGGCGGAGCCCCGCCCAGAACGTCAGGACGCCGCTCCAGAGCGTCGTCTCCCT
CCCCCTCAGACCCAACACCTCTCCCGCCCACGGGGGCGCCTACGTGATGCACGGGGAGCGGGAAGAGAGCAAAGGCTAGT
ATCGCGAGTACGCGGACAGCAACCGGAAGCAGGTCCCGGGGACGACGGCGCACGCGGAGCGGGGCGGCGTGCAGGTGCCC
ACCACGCCGGCCGGGTCCTGCGTGAAGACCGGGACCCCGGCGCCC

Alignment

ORF - retro_ttru_98 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 54.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTK
          P.....PSER..P.QNVRT.L.SV.SL...PNT.SPA...A.VM.....ESKG..REY.D..RKQV.GT.
Retrocopy PRQSMTPSERRSPAQNVRTPLQSVVSLPLRPNT-SPAHGGAYVMHGEREESKG*YREYADSNRKQVPGTT

Parental  VDAERDGVKVPTTLAEYCVKTKAPAP
          ..AER.GV.VPTT.A..CVKT..PAP
Retrocopy AHAERGGVQVPTTPAGSCVKTGTPAP

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_98 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_98 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023874	1 retrocopy	retro_cpor_743,
Macropus eugenii	ENSMEUG00000000812	1 retrocopy	retro_meug_1683,
Mus musculus	ENSMUSG00000020307	1 retrocopy	retro_mmus_23,
Ochotona princeps	ENSOPRG00000001017	1 retrocopy	retro_opri_464,
Pan troglodytes	ENSPTRG00000010153	1 retrocopy	retro_ptro_52,
Rattus norvegicus	ENSRNOG00000008348	1 retrocopy	retro_rnor_1464,
Ictidomys tridecemlineatus	ENSSTOG00000023255	1 retrocopy	retro_itri_822,
Tursiops truncatus	ENSTTRG00000000391	2 retrocopies	retro_ttru_1142, retro_ttru_98 ,
Tursiops truncatus	ENSTTRG00000000595	1 retrocopy	retro_ttru_1578,
Tursiops truncatus	ENSTTRG00000010587	1 retrocopy	retro_ttru_724,