RetrogeneDB ID: retro_ttru_1923

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_98803:236158..236425(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM42
• Ensembl ID: ENSTTRG00000004623
• Aliases: None
• Description: transmembrane protein 42 [Source:HGNC Symbol;Acc:28444]

Sequence

>retro_ttru_1923
CACTTCCCAGCCTGCACGCTGTGGTACCACTTCTGGGGCGTGCTCAAACTGCCTGTGCGCATGCGCATTCAGGGCCCTGG
CGCAGCTTCCAACGCGCAGGTCTTCAGCAGCGAGGTGAGTATGGGATTCTGCTTATCCGGCTTAGGCGTCCTCGTGATGG
CTACCACCAATTCTCTCACGTGAATGTTCGTTAGCCGGAGCCTCAATTTCACCACATCTTCGGCCATTGCATCTGTCATG
GTGACTTTTTCAAATATCCTCAGCTCA

Alignment

ORF - retro_ttru_1923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.96 %
• Parental protein coverage: 55.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HLQAGAMRRRFWGVF-NCLCAGAFGALA-AASAKLAFGSEVVNVGFCV--LGIIVMATTNSLMWTFFSRG
          H..A......FWGV..NCLCA.AF.ALA.AAS....F.SEV...GFC...LG..VMATTNSL...F.SR.
Retrocopy HFPACTLWYHFWGVL>NCLCACAFRALA<AASNAQVFSSEV-SMGFCLSGLGVLVMATTNSLT*MFVSRS

Parental  LSFSMSSAIASVTVTFSNILSS
          L.F..SSAIASV.VTFSNILSS
Retrocopy LNFTTSSAIASVMVTFSNILSS

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_1923 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1923 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000029706	3 retrocopies	retro_mdom_1139, retro_mdom_1400, retro_mdom_406,
Tursiops truncatus	ENSTTRG00000004623	1 retrocopy	retro_ttru_1923 ,