RetrogeneDB ID: retro_ttru_855

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_375:177859..178512(+)
• Located in intron of: ENSTTRG00000010845

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_855
GTGGTAGCCGTGGCAGTATTTTTACTGACATTCTATGTTATTTCTCAAGCATTTGAAATAAAAATGGATGTGAGTTTAGG
AAATCTATTTGCAAGGTCAGCAATGTACGCAGTTGCACGTTCCACAAAACCTCCCAGGTATAAATGTGGGATCTCAAAAG
CTTGCCCTGAGAAGCATTTGCTTTTAAAATGGCAAGTGGAGCAGCCAGTGTGGTAGGACCCAAAATCTGCCTGGAGAAGA
ATGTTTTAATGAGTGGTGTTAAGAATAATGTTGGAAGAGGAATCAATGTTGCCTAGGTAAATGGAAAAACAGGAGATCTA
ATAGACACCAGATATTTTGACATGTGGGGAGGAAATGTGGCCTCATTTATTGAGTTTCTGAAGGCCATACAAGATGGAAC
AATAGTCTTACTGGGAACATATGATGATGGAGCAACCCAAACTCAATGATGAGGCCCGGCAGCTCATTGCTGAACTGGGG
AGTACATCTACTACTCATCTTGTTTTAGAGACAACTGGGTCTTCTGTGGTGGAAAAGGCATTAAGAAAAAAAGGCCTTTT
GAACAGCACATAAAGAGCAATAAGGACACAAACAAATATGAAGGATGGCCCGAAGTTGTAGAAATGGAAGGATGCATTCC
CCAGAAGCAAGAC

Alignment

ORF - retro_ttru_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.86 %
• Parental protein coverage: 96.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVAVAVFLLTFYVISQVFEIKMDASLRNLFARSALDAVARSTKPPRYKCGISKACPEKH-FAFKMASGAA
          VVAVAVFLLTFYVISQ.FEIKMD.SL.NLFARSA..AVARSTKPPRYKCGISKACPEKH.FAFKMASGAA
Retrocopy VVAVAVFLLTFYVISQAFEIKMDVSLGNLFARSAMYAVARSTKPPRYKCGISKACPEKH<FAFKMASGAA

Parental  NVVGPKICLEDNVLMSGVKNNVGRGINVA-VNGKTGDLIDTRYFDMWGGNVAPFIEFLKAIQDGTIVLMG
          .VVGPKICLE.NVLMSGVKNNVGRGINVA.VNGKTGDLIDTRYFDMWGGNVA.FIEFLKAIQDGTIVL.G
Retrocopy SVVGPKICLEKNVLMSGVKNNVGRGINVA*VNGKTGDLIDTRYFDMWGGNVASFIEFLKAIQDGTIVLLG

Parental  TYDDGAT-KLNDEARQLIAELGSTSITHL-GFRDNWVFCGGKGIKTKSPFEQHIKNNKDTNKYEGWPEVV
          TYDDGAT.KLNDEARQLIAELGSTS.THL..FRDNWVFCGGKGIK.K.PFEQHIK.NKDTNKYEGWPEVV
Retrocopy TYDDGAT>KLNDEARQLIAELGSTSTTHL<CFRDNWVFCGGKGIKKKRPFEQHIKSNKDTNKYEGWPEVV

Parental  EMEGCIPQKQD
          EMEGCIPQKQD
Retrocopy EMEGCIPQKQD

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_855 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_855 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 ,