RetrogeneDB ID: retro_ttru_1385

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111907:53685..54490(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFDP1
• Ensembl ID: ENSTTRG00000001215
• Aliases: None
• Description: craniofacial development protein 1 [Source:HGNC Symbol;Acc:1873]

Sequence

>retro_ttru_1385
ATGGAGGAATTCGACTCTGAAGATTTCTCCACCTCGGAGGAGGACGAGGACTACGTGTCATCGGGTGGAGAGTATAGTGA
AGATGATGTAAATGAATTAGTGAAGGAAGATGAAGTGGATGGTGAAGAGAAGACACAGAAAACCAAAGGGAGAAAAAGAA
AGGCTCAGAGCATTCTGGCCAGGAAGAGAAAGCAAGGTGGCCTCTCATTAGAAAAGGACGAGAAGGATGCCAGCGAGGAA
TCTGGAGGAAGAAGTAGTGAGGAGGAAGATGTAGCTGCAGAGCAAGAAAAAGGCATTGAGTCAGAGGATACGAGGAAAAA
GAAGGAAGATGAACTATGGGCCAGCTTCCTCAATGACGTAGGACTAAAATCAAAAGTGCCTCCTTGTACACAAGTTAAAA
GAGGAGAGGAGGCTGAAGAGACAAGTTCAAGTAAATTGTTGGTCAAAGCAGAAGAGCTAGAGAAACCTAAAGAAACAGAA
AAAGTTAAAATCACCAAGGTGTTTGATTTTGCTGGTGAAGTCAGGGTGACTAAGGAAGTGGATGCTACATCTAAAGAAGC
CAAATCCTTCTTCAAGCAAAATGCGAAAGAAAAATCCCCAGGCTAATAATGTCCCTTCAGCTCTACCGTCACTTCCTGCC
GGGTCAGGGTTAAAAAGGTCAAGGGATATGAGCAGCCTTTTGGGGAAAATAGGAGCCAAGAAGCAGAAGATGAGCACACT
AGAGAAGGCCGAGCTGGACTGGGAGAGCTTCAAGGAGGAAGAGGGCATTGGAGAAGAACTAGCCATCCACAATCGAGGGA
AGGAG

Alignment

ORF - retro_ttru_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.93 %
• Parental protein coverage: 89.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEEFDSEDFSTSEEDEDYVPSGGEYSEDDVNELVKEDEVDGEEQTQKTKERKRKSQSIPARKRKQGGLSL
          MEEFDSEDFSTSEEDEDYV.SGGEYSEDDVNELVKEDEVDGEE.TQKTK.RKRK.QSI.ARKRKQGGLSL
Retrocopy MEEFDSEDFSTSEEDEDYVSSGGEYSEDDVNELVKEDEVDGEEKTQKTKGRKRKAQSILARKRKQGGLSL

Parental  EEEDEEDANEESGGSSSEEEDGAAEPEKGIESEDAKKKKEDELWASFLNDVGPKSKVPXXXXXXRREEAE
          E..DE.DA.EESGG.SSEEED.AAE.EKGIESED..KKKEDELWASFLNDVG.KSKVP......R.EEAE
Retrocopy EK-DEKDASEESGGRSSEEEDVAAEQEKGIESEDTRKKKEDELWASFLNDVGLKSKVPPCTQVKRGEEAE

Parental  ETSSSKLLVKAEELEKPKETEKVKITKVFDFAGEEVRVTKEVDATSKEAKSFFKQNEKEK-PQA-NVPSA
          ETSSSKLLVKAEELEKPKETEKVKITKVFDFAGE.VRVTKEVDATSKEAKSFFKQN.KEK.PQA.NVPSA
Retrocopy ETSSSKLLVKAEELEKPKETEKVKITKVFDFAGE-VRVTKEVDATSKEAKSFFKQNAKEK>PQANNVPSA

Parental  LPSLPAGSGLKRSSGMSSLLGKIGAKKQKMSTLEKSKLDWESFKEEEGIGEELAIHNRGKE
          LPSLPAGSGLKRS..MSSLLGKIGAKKQKMSTLEK..LDWESFKEEEGIGEELAIHNRGKE
Retrocopy LPSLPAGSGLKRSRDMSSLLGKIGAKKQKMSTLEKAELDWESFKEEEGIGEELAIHNRGKE

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_1385 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1385 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000695	1 retrocopy	retro_cpor_465,
Dasypus novemcinctus	ENSDNOG00000013266	2 retrocopies	retro_dnov_2442, retro_dnov_2546,
Echinops telfairi	ENSETEG00000016429	1 retrocopy	retro_etel_1574,
Myotis lucifugus	ENSMLUG00000000890	1 retrocopy	retro_mluc_2525,
Rattus norvegicus	ENSRNOG00000019326	1 retrocopy	retro_rnor_2289,
Ictidomys tridecemlineatus	ENSSTOG00000004124	2 retrocopies	retro_itri_1117, retro_itri_1815,
Tupaia belangeri	ENSTBEG00000015362	2 retrocopies	retro_tbel_1305, retro_tbel_2189,
Tursiops truncatus	ENSTTRG00000001215	1 retrocopy	retro_ttru_1385 ,