RetrogeneDB ID: retro_ttru_1096

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_102799:12344..13064(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEAD1
• Ensembl ID: ENSTTRG00000006621
• Aliases: None
• Description: TEA domain family member 1 (SV40 transcriptional enhancer factor) [Source:HGNC Symbol;Acc:11714]

Sequence

>retro_ttru_1096
AAAGTTCGAGATATTCAAGCCGCCATTAAGGTGTCACATTCTAGTCACATTCAGGTTCTTGCCAGAAGGAAATCTTGTGA
TTTTCGTTCCAAGCTAAAGGATCAGACTGCAAAGGATAAGGCTCAGCAGCACATGGCCGCCATGTCCTCAGCCCAGATCG
TATCAGCCACTGCCATTTACAGCAAGCTGGGGCTGCCAGGGATTCCACACCCCACCTTCCCAGGGGCGTCGGGGTTCTGG
TCGGGAATGATACAAACAGGACAGCCTGGATCCTCGCAAGACGTCAAGCCCTTCGTGCAGCAGGCCTACCCCATCCAGCC
AGCGGTCACAGCCCCCATCCCAGGGTTTGAGCCTGCGTCAGCCCCAGCTCCCTCGGTCCCGGCCTAGCAGGGCCGCTCCA
TTGGCACAACCAAACTCCGCCTGGTGGAGTTCTCAGCCTTCCTCAAACAGCAGCGAGACCCTGACTCGTACAACAAACAC
CTATTCGTGCACATTGGGCATGCCAACCATTCTTACAGTGACCCATTGCTCTAATCAGTGGACATTCGTCAGATTTATGA
CAAATTTCCTGAAAAGAAAGGTGTCTTAAAGGAACTGTTTGGAAAGGGCCTTCAAAATGCCTTCTTCCTCGTAAAATTCT
GGGCTGATTTAAACTGCGGTATTCAAGATGATGCCGGGACTTTTTACGGCGTGACCAGTCAGTATGAGAGTTCTGAGAAT

Alignment

ORF - retro_ttru_1096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.17 %
• Parental protein coverage: 56.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLRTGKTRTRKQVSSHIQVLARRKSRDFHSKLKDQTAKDKALQHMAAMSSAQIVSATAIHNKLGLPGIPR
          K.R..........SSHIQVLARRKS.DF.SKLKDQTAKDKA.QHMAAMSSAQIVSATAI..KLGLPGIP.
Retrocopy KVRDIQAAIKVSHSSHIQVLARRKSCDFRSKLKDQTAKDKAQQHMAAMSSAQIVSATAIYSKLGLPGIPH

Parental  PTFPGAPGFWPGMIQTGQPGSSQDVKPFVQQAYPIQPAVTAPIPGFEPASAPAPSVPAWQGRSIGTTKLR
          PTFPGA.GFW.GMIQTGQPGSSQDVKPFVQQAYPIQPAVTAPIPGFEPASAPAPSVPA.QGRSIGTTKLR
Retrocopy PTFPGASGFWSGMIQTGQPGSSQDVKPFVQQAYPIQPAVTAPIPGFEPASAPAPSVPA*QGRSIGTTKLR

Parental  LVEFSAFLEQQRDPDSYNKHLFVHIGHANHSYSDPLLESVDIRQIYDKFPEKKGGLKELFGKGPQNAFFL
          LVEFSAFL.QQRDPDSYNKHLFVHIGHANHSYSDPLL.SVDIRQIYDKFPEKKG.LKELFGKG.QNAFFL
Retrocopy LVEFSAFLKQQRDPDSYNKHLFVHIGHANHSYSDPLL*SVDIRQIYDKFPEKKGVLKELFGKGLQNAFFL

Parental  VKFWADLNCSIQDDAGAFYGVTSQYESSEN
          VKFWADLNC.IQDDAG.FYGVTSQYESSEN
Retrocopy VKFWADLNCGIQDDAGTFYGVTSQYESSEN

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_1096 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1096 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010263	1 retrocopy	retro_cjac_193,
Tupaia belangeri	ENSTBEG00000017462	1 retrocopy	retro_tbel_4523,
Tarsius syrichta	ENSTSYG00000001514	1 retrocopy	retro_tsyr_657,
Tursiops truncatus	ENSTTRG00000006621	1 retrocopy	retro_ttru_1096 ,