RetrogeneDB ID: retro_ttru_1888

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_97381:112879..113413(+)
• Located in intron of: ENSTTRG00000004826

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPD52
• Ensembl ID: ENSTTRG00000000088
• Aliases: None
• Description: tumor protein D52 [Source:HGNC Symbol;Acc:12005]

Sequence

>retro_ttru_1888
GGTCTACTGAGAACAGACCCAGTACCCGAGGAAGGAGAAGATGTTGCTGCCACTATCGGTGCCACTGAAACCCTATCAGA
GGAGGAGCGAGAAGAGCTAAGAAGAGAACTTGCTAAGGTAGAAGAAGAAATGCAGACTCTGTCTCAAGTGTTAGCAGAAA
AAGGAAAGCACCTAACAGAGATCAAGCGGAAACTTGGGATCAATTCACTACAGACACTAAAACAGAACATTGCCAAAGGG
TGGCAAGATGTGACAGCCACGTCTGCGTACAAGAAGACCTCTGAAACCTTATCTCAGCCTGGACAAAAGGCTTCAGCTGC
TTTTTCATCTGTTGGATCAGTCATCACCAAAAAGCTGGAAGATGTAAAAAACTCCCCAACTTTCAAATAATTTGAGGAAA
GGGTTGAAAACTTAAAGTCTAAAGTAGGGGGAACCAAGCCTGCTGGTGGTGATTTTGGAGAATTCTTGAATTCGACTGCA
AACGCTAGTTCCACCACCACGGAGCCTCTTCCAGAAGAGACACAGGAGAGCCTG

Alignment

ORF - retro_ttru_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 78.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLLRTDPVPEEGEDVVATISATETLSEEEREELRRELAKVEEEIQTLSQVLAAKEKHLTEIKRKLGINSL
          GLLRTDPVPEEGEDV.ATI.ATETLSEEEREELRRELAKVEEE.QTLSQVLA.K.KHLTEIKRKLGINSL
Retrocopy GLLRTDPVPEEGEDVAATIGATETLSEEEREELRRELAKVEEEMQTLSQVLAEKGKHLTEIKRKLGINSL

Parental  QELKQNIAKGWQDVTATSAYKKTSETLSQAGQKASAAFSSVGSVITKKLEDVKNSPTFKSFEEKVENLKS
          Q.LKQNIAKGWQDVTATSAYKKTSETLSQ.GQKASAAFSSVGSVITKKLEDVKNSPTFK.FEE.VENLKS
Retrocopy QTLKQNIAKGWQDVTATSAYKKTSETLSQPGQKASAAFSSVGSVITKKLEDVKNSPTFK*FEERVENLKS

Parental  KVGGTKPAGGDFGEVLNSTANASSTTTEPLPEQAQESL
          KVGGTKPAGGDFGE.LNSTANASSTTTEPLPE..QESL
Retrocopy KVGGTKPAGGDFGEFLNSTANASSTTTEPLPEETQESL

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_1888 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1888 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001357	1 retrocopy	retro_chof_1370,
Mus musculus	ENSMUSG00000027506	1 retrocopy	retro_mmus_3221,
Oryctolagus cuniculus	ENSOCUG00000008247	1 retrocopy	retro_ocun_325,
Otolemur garnettii	ENSOGAG00000016601	2 retrocopies	retro_ogar_1677, retro_ogar_348,
Tursiops truncatus	ENSTTRG00000000088	1 retrocopy	retro_ttru_1888 ,