RetrogeneDB ID: retro_ttru_1086

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_102342:222443..222947(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDDC2
• Ensembl ID: ENSTTRG00000002258
• Aliases: None
• Description: HD domain containing 2 [Source:HGNC Symbol;Acc:21078]

Sequence

>retro_ttru_1086
ATGGCTGCGCCCATCTCGGGCCACGGGGCCTAGAACCTGCTGCAGTTCCTGCGGCTGGTGGGACAGCTCAAGAGAGTCCC
ATGTACTGGCTGGGCATACAGAAATGTCCAGAAGCCAGAGAGCATATCAGGTCACATGTATAGGATGGCAATTATGGATC
TGGTGACCAAAGATGAACATCTTAACAAAGACCGATGTGTACGCCTAGCTCTGGTTCATGATTTGACAGAATGCATCGCT
GGGGACATAGCACCAGCAGATAACATCCCCAAAGAGGAAAAACATAGGCGAGAAGAGGAAGCTATGAAGCAGCTAACCCA
GCTACTCCCAGAGGATCTCAGAAAAGAGCTCTATGAACTTTGGAAAGAATATGAGACCCAATCTAGTGCAGAAGTTAAAT
CTGTGAAGCAGCTGGACCAATGTGAAATGATTCTTCAGGCATCTGAATATGAAGACCTTGAGAACAAACCTGGGAGACTG
CAGGACTTCTACAAGTCCACAGCA

Alignment

ORF - retro_ttru_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPISGRGARDLLQFLRLVGQLKRVPRTGWVYRNVQKPESVSDHMYRMAVMALVTKDEHLNKDRCVRLA
          MAAPISG.GA..LLQFLRLVGQLKRVP.TGW.YRNVQKPES.S.HMYRMA.M.LVTKDEHLNKDRCVRLA
Retrocopy MAAPISGHGA*NLLQFLRLVGQLKRVPCTGWAYRNVQKPESISGHMYRMAIMDLVTKDEHLNKDRCVRLA

Parental  LVHDMAECIVGDIAPADNIPKEEKHRREEEAMKQLTQLLPEDLRKELYELWEEYETQSSAEAKFVKQLDQ
          LVHD..ECI.GDIAPADNIPKEEKHRREEEAMKQLTQLLPEDLRKELYELW.EYETQSSAE.K.VKQLDQ
Retrocopy LVHDLTECIAGDIAPADNIPKEEKHRREEEAMKQLTQLLPEDLRKELYELWKEYETQSSAEVKSVKQLDQ

Parental  CEMILQASEYEDLENKPGRLQDFYNSTA
          CEMILQASEYEDLENKPGRLQDFY.STA
Retrocopy CEMILQASEYEDLENKPGRLQDFYKSTA

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_1086 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1086 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
Ailuropoda melanoleuca	ENSAMEG00000009635	1 retrocopy	retro_amel_1399,
Canis familiaris	ENSCAFG00000001030	1 retrocopy	retro_cfam_2179,
Microcebus murinus	ENSMICG00000014059	1 retrocopy	retro_mmur_549,
Tupaia belangeri	ENSTBEG00000011826	1 retrocopy	retro_tbel_4277,
Tursiops truncatus	ENSTTRG00000002258	1 retrocopy	retro_ttru_1086 ,