RetrogeneDB ID: retro_ttru_1219

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_107456:392949..393339(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM3C
• Ensembl ID: ENSTTRG00000016229
• Aliases: None
• Description: family with sequence similarity 3, member C [Source:HGNC Symbol;Acc:18664]

Sequence

>retro_ttru_1219
AATAATGTTGGAAGACAGATCAATGTTGCCTTGGTAAGTGGAAAAACAGGAGATCTAATAGACACCAGGTATTTTGACAT
GTGTAGAAGAAATGTGGCCTCATTTATTGAGTTTCTGAAGGCCATACAAGGTGGAACAATAGTCTTACTGGGAGCATATG
ATGATGGAGCTACCAAACTCAATGATGAGGGCTGACAACTCATTGCTGAATTGGGGAGTACACCTATTACTCATCTTGGT
TTTAGAGACTAATGGGTCTTATGTGGTGGAAAAGGCATTAAGACAAAAAGCCCTTTTGAACAGCACATAAAGAACTATAA
GGACACAAAGAAATATGAAGGATGGCCTGAAGTTGCAGAGATCAAAGGATGCATCCCCCAGAAGCAAGAC

Alignment

ORF - retro_ttru_1219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.15 %
• Parental protein coverage: 57.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NNVGRGINVA-VNGKTGDLIDTRYFDMWGGNVAPFIEFLKAIQDGTIVLMGTYDDGATKLNDEARQLIAE
          NNVGR.INVA.V.GKTGDLIDTRYFDM...NVA.FIEFLKAIQ.GTIVL.G.YDDGATKLNDE..QLIAE
Retrocopy NNVGRQINVALVSGKTGDLIDTRYFDMCRRNVASFIEFLKAIQGGTIVLLGAYDDGATKLNDEG*QLIAE

Parental  LGSTSITHLGFRDNWVFCGGKGIKTKSPFEQHIKNNKDTNKYEGWPEVVEMEGCIPQKQD
          LGST.ITHLGFRD.WV.CGGKGIKTKSPFEQ.............WPEV.E..GCIPQKQD
Retrocopy LGSTPITHLGFRD*WVLCGGKGIKTKSPFEQXXXXXXXXXXXXXWPEVAEIKGCIPQKQD

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_1219 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1219 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003224	1 retrocopy	retro_chof_1467,
Felis catus	ENSFCAG00000023087	1 retrocopy	retro_fcat_1392,
Homo sapiens	ENSG00000196937	1 retrocopy	retro_hsap_4657,
Loxodonta africana	ENSLAFG00000010029	1 retrocopy	retro_lafr_1169,
Macropus eugenii	ENSMEUG00000006906	2 retrocopies	retro_meug_2057, retro_meug_536,
Monodelphis domestica	ENSMODG00000015478	1 retrocopy	retro_mdom_1392,
Sarcophilus harrisii	ENSSHAG00000015103	1 retrocopy	retro_shar_6,
Tursiops truncatus	ENSTTRG00000016229	2 retrocopies	retro_ttru_1219 , retro_ttru_855,