RetrogeneDB ID: retro_ttru_1759

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_90628:127430..128022(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD2
• Ensembl ID: ENSTTRG00000003450
• Aliases: None
• Description: COMM domain containing 2 [Source:HGNC Symbol;Acc:24993]

Sequence

>retro_ttru_1759
CTGGTCCTGTCAGAGGAGCACAAGGAGCACCTGGCCTTCCTGCCTCAAGTGGACAGCACGGTGGTCTCTGAGTTTGGGCG
AATTGTGGTGGAGTTCCCGAGGTGAGGCTCGAACCCCAAGATCTACGAAGGCGCTGCGAGAAAGCTCAGTGTGAGTAGTG
ACACTGTCCAACATGGTGTGGAAGAATTTAATATACCTCCTTCACTGAAAGTTCAAAGCTTTATGATTTCTGAACTGGAT
TTCCAAGACTGTTTTTGTTCTGTGATCCTCTGAAGAATTGAACAAACTGTTGCTTCAGCTTTTTCTGGACAACAGAAAGG
AGATCAGAACTATCCTGAGTGAATCAGCACCAGACCTCCCCAGTTACCACAGCCCTTGAATGGCGACTAGATGTACAGCT
TGCAAGCAGAAGCCTCAGGCAACAGATTAAACCAACAGTGACTATAAAGCTACACCTTAATAGAATGGAGGTCATAACAC
CCAAGTTCTGCAGACACACCCAGCCACCCTGCTCCATTTGGTTCAGCAATTGGAGCAAGCCTTGAAGGAGATGAAAACAG
ACCACCGTAGGAGAGCTGTGCGCAATATCAAG

Alignment

ORF - retro_ttru_1759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.5 %
• Parental protein coverage: 98.99 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNLSKEHKEHLALPAQVNSAVVLEFGRIAVKFLRRASNPKIYXXXXXKLSVSSDTVQHGVE-GLIHLLTE
          L.LS.EHKEHLA...QV.S.VV.EFGRI.V.F.R..SNPKIY.....KLSVSSDTVQHGVE..LI.LL..
Retrocopy LVLSEEHKEHLAFLPQVDSTVVSEFGRIVVEFPR*GSNPKIYEGAARKLSVSSDTVQHGVE>NLIYLLH*

Parental  SSKLMISELDFQDSVFVLGFSEELNKLLLQLYLDNRKEIRTILSELAPDLPSYHS-LEWRLDVQLASRSL
          ..K...........VFVL..SEELNKLLLQL.LDNRKEIRTILSE.APDLPSYHS.LEWRLDVQLASRSL
Retrocopy KFKAL*FLNWISKTVFVL*SSEELNKLLLQLFLDNRKEIRTILSESAPDLPSYHS>LEWRLDVQLASRSL

Parental  RQQMKPSVTIKLHLNQ-NGDHNTQVLQTDPATLLHLVQQLEQALEEMKTNHCRRVVRNIK
          RQQ.KP.VTIKLHLN..NG.HNTQVLQT.PATLLHLVQQLEQAL.EMKT.H.RR.VRNIK
Retrocopy RQQIKPTVTIKLHLNR<NGGHNTQVLQTHPATLLHLVQQLEQALKEMKTDHRRRAVRNIK

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_1759 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1759 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013809	1 retrocopy	retro_chof_1601,
Cavia porcellus	ENSCPOG00000005273	2 retrocopies	retro_cpor_520, retro_cpor_956,
Rattus norvegicus	ENSRNOG00000043386	1 retrocopy	retro_rnor_2231,
Ictidomys tridecemlineatus	ENSSTOG00000010888	4 retrocopies	retro_itri_180, retro_itri_1803, retro_itri_1880, retro_itri_1899,
Tupaia belangeri	ENSTBEG00000003545	1 retrocopy	retro_tbel_2895,
Tursiops truncatus	ENSTTRG00000003450	1 retrocopy	retro_ttru_1759 ,