RetrogeneDB ID: retro_ttru_403

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2144:265656..266088(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC1
• Ensembl ID: ENSTTRG00000010306
• Aliases: None
• Description: trafficking protein particle complex 1 [Source:HGNC Symbol;Acc:19894]

Sequence

>retro_ttru_403
ACTGTCCACAACCTGTACCTGTTTGACCGGAATGGAGCGTGTCTGCATTACTGTGAGTGGCACCGCAAGAAGCAAGCAGA
GATCCCCAAGTAGGAGGAGTACAAGCTGATGTACGGGATGCTCTTCTCTATCCTTTCCTTTGTCAGCAAAATGTCCCCAC
TAGACATTAAGGACGGCTTCCTGGCCTTCCAAACTAGACGTTACAAACTCCATTAGTACGAGATGCCCGCTGGGATCAGC
GCTGTCATGAATACTGACTTGGCCGTGGGACCCATCTGAGATGTGCTGCACCACATCCACGGTGAGCTGTACGTGGAGCT
GGTGGTGAAGAATCCCCTGTGCTCGCTGGGCCAAACTGTGCAGAATGAGCTCTTCCGCTCCCGACTGGACTCCTGTGGCC
ACTCTCCGCCCTTCTTCTCCACCCGGGCTGGC

Alignment

ORF - retro_ttru_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TVHNLYLFDRNGVCLHYSEWHRKKQAGIPKEEEYKLMYGMLFSIRSFVSKMSPLDMKDGFLAFQTSRYKL
          TVHNLYLFDRNG.CLHY.EWHRKKQA.IPK.EEYKLMYGMLFSI.SFVSKMSPLD.KDGFLAFQT.RYKL
Retrocopy TVHNLYLFDRNGACLHYCEWHRKKQAEIPK*EEYKLMYGMLFSILSFVSKMSPLDIKDGFLAFQTRRYKL

Parental  HYYETPTGIKVVMNTDLGVGPIRDVLHHIYSALYVELVVKNPLCPLGQTVQSELFRSRLDSYVRSLPFFS
          H.YE.P.GI..VMNTDL.VGPI.DVLHHI...LYVELVVKNPLC.LGQTVQ.ELFRSRLDS...S.PFFS
Retrocopy H*YEMPAGISAVMNTDLAVGPI*DVLHHIHGELYVELVVKNPLCSLGQTVQNELFRSRLDSCGHSPPFFS

Parental  ARAG
          .RAG
Retrocopy TRAG

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_403 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_403 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047214	1 retrocopy	retro_btau_280,
Callithrix jacchus	ENSCJAG00000014756	1 retrocopy	retro_cjac_1057,
Erinaceus europaeus	ENSEEUG00000004320	1 retrocopy	retro_eeur_665,
Sorex araneus	ENSSARG00000010582	1 retrocopy	retro_sara_590,
Tursiops truncatus	ENSTTRG00000010306	1 retrocopy	retro_ttru_403 ,