RetrogeneDB ID: retro_ttru_1404

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112491:56317..56860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS29
• Ensembl ID: ENSTTRG00000015090
• Aliases: None
• Description: vacuolar protein sorting 29 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14340]

Sequence

>retro_ttru_1404
TTGGTGTTGGTATTAGGAGACCTGCACATCCCACACTGGAGCAACAGTTTGCCAGCTAAATTCAAAAAACTGCTGGTGCC
AGGAATGATTCAGCACACTCTCTGCACTGGAAACCTTTGTACCGAAGAGAGTTATGACTATCTCCAGACTCTGGCTGGCG
ATGTTCATATTGTGAGAGGAGACTTCAATGAGAATCTGAATTATCAAGAACAGAAAGTCGTTAACTGTTGGGCAGTTCAA
AATTGGTTTGATCCATGGACATCAAGTTATTCCATGGGGAGATATGGCCAGCTTAGCTCTGTTGCAGAGGCAGTTTGATG
TGGATATTCTTATTTCAGGACACACAGAAATATTTGAACATTTGAGCATGAAAATAAAGTCTACATTAATCCAGGTTCTG
CCACAGGAGCATATAATGCCTTGGAAACAAACATTATTCCTTCATTTGTGTTGATGGATATCCAGGCTTCTACACTTGTC
ACTTGTGTGTATCAGCTAATTAGAGACGTCCTGAAAGTAGAACGAATCGAATACAAAAAATCA

Alignment

ORF - retro_ttru_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.62 %
• Parental protein coverage: 97.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPE
          LVLVLGDLHIPH..NSLPAKFKKLLVPG.IQH.LCTGNLCT.ESYDYL.TLAGDVHIVRGDF.ENLNY.E
Retrocopy LVLVLGDLHIPHWSNSLPAKFKKLLVPGMIQHTLCTGNLCTEESYDYLQTLAGDVHIVRGDFNENLNYQE

Parental  QKVV-TVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE-AFEHENKFYINPGSATGAY
          QKVV.TVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHT..FE..FEHENK.YINPGSATGAY
Retrocopy QKVV>TVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTEIFE<TFEHENKVYINPGSATGAY

Parental  NALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS
          NALETNIIPSFVLMDIQAST.VT.VYQLI.D..KVERIEYKKS
Retrocopy NALETNIIPSFVLMDIQASTLVTCVYQLIRDVLKVERIEYKKS

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_1404 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1404 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001891	1 retrocopy	retro_acar_30,
Felis catus	ENSFCAG00000004135	2 retrocopies	retro_fcat_165, retro_fcat_848,
Loxodonta africana	ENSLAFG00000006176	1 retrocopy	retro_lafr_1115,
Oryctolagus cuniculus	ENSOCUG00000011924	1 retrocopy	retro_ocun_1611,
Tupaia belangeri	ENSTBEG00000012756	4 retrocopies	retro_tbel_1121, retro_tbel_2187, retro_tbel_330, retro_tbel_4424,
Tursiops truncatus	ENSTTRG00000015090	2 retrocopies	retro_ttru_1404 , retro_ttru_1492,