RetrogeneDB ID: retro_ttru_68

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1114:185946..186239(-)
• Located in intron of: ENSTTRG00000012442

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000002964
• Aliases: None
• Description: None

Sequence

>retro_ttru_68
GAGCTGTTTGCAGACAAAGTTCAAAGACAGCAGAAAACTTTCATGCTCTGAGCACTGGGGAGAAAGGCTTTGGTTATAAA
GGTTCCTGCTTTCACAGAATAATTCCGGGATTTCTGTGCCAGGGTGGTGACTTCACATGCCATAATGGCACTGGTGGCAA
GTCCATCTATGGGGAGAAATTTGCTGATGAGAATTTCCTCCTGAAGCATACGGGTCCTGGCATCTTGTCCATGGCAAATG
CTGGCCCCAACACAAACGGTTCCCAGTTTTTCATCTGCACTGCCAAGACTGAG

Alignment

ORF - retro_ttru_68 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.94 %
• Parental protein coverage: 81.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELFADKVP-KTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFDDENFLLK
          ELFADKV..KTAENF.ALSTGEKGFGYKGSCFHRIIPGF.CQGGDFT.HNGTGGKSIYGEKF.DENFLLK
Retrocopy ELFADKVQ<KTAENFHALSTGEKGFGYKGSCFHRIIPGFLCQGGDFTCHNGTGGKSIYGEKFADENFLLK

Parental  HTGPGILSMANAGPNTNGSQFFICTAKTE
          HTGPGILSMANAGPNTNGSQFFICTAKTE
Retrocopy HTGPGILSMANAGPNTNGSQFFICTAKTE

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_68 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_68 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 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011597	12 retrocopies	retro_chof_1071, retro_chof_1276, retro_chof_1317, retro_chof_1335, retro_chof_1876, retro_chof_1955, retro_chof_1959, retro_chof_2687, retro_chof_336, retro_chof_632, retro_chof_652, retro_chof_929,
Monodelphis domestica	ENSMODG00000016089	9 retrocopies	retro_mdom_1373, retro_mdom_1524, retro_mdom_1856, retro_mdom_1884, retro_mdom_215, retro_mdom_272, retro_mdom_29, retro_mdom_730, retro_mdom_85,
Tursiops truncatus	ENSTTRG00000002964	16 retrocopies	retro_ttru_1176, retro_ttru_1177, retro_ttru_1178, retro_ttru_1232, retro_ttru_1294, retro_ttru_1372, retro_ttru_1429, retro_ttru_1571, retro_ttru_222, retro_ttru_287, retro_ttru_298, retro_ttru_503, retro_ttru_623, retro_ttru_68 , retro_ttru_763, retro_ttru_906,
Tursiops truncatus	ENSTTRG00000014385	1 retrocopy	retro_ttru_1314,