RetrogeneDB ID: retro_itri_795

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393324.1:1794470..1794718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC6B
• Ensembl ID: ENSSTOG00000002897
• Aliases: None
• Description: trafficking protein particle complex 6B [Source:HGNC Symbol;Acc:23066]

Sequence

>retro_itri_795
ACAAAAGACATTGCAAAGTTCAAGGCTGACTTAGATAGGATGAAGTTTATTTGTAAAGATTTTGGGCTACGGTTTTCAGG
AAGCAAACTGACAATCTAAGGACAGATCATTTGAGCATTTTTGCACTTAGGGACAAAAAGTTTCATCTGCTTGCTCAGAT
ATCTGCAGGAAAACAGTACTTAGAACGCACCTCGACACATTTAGCATTTCCATGTGGTTTCATCCCAAGGGGCTTCTCAA
ACTCGGGT

Alignment

ORF - retro_itri_795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 52.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TKDTARFKDELGIMKFICKDF-WTTVFKKQIDNLRTNHQGIYVLQDNKFRLLTQMSAGKQYLEHASKYLA
          TKD.A.FK..L..MKFICKDF.W.TVF.KQ.DNLRT.H..I..L.D.KF.LL.Q.SAGKQYLE..S..LA
Retrocopy TKDIAKFKADLDRMKFICKDF<WATVFRKQTDNLRTDHLSIFALRDKKFHLLAQISAGKQYLERTSTHLA

Parental  FTCGLIRGGLSNLG
          F.CG.I..G.SN.G
Retrocopy FPCGFIPRGFSNSG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_795 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_795 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013828	1 retrocopy	retro_etel_1104,
Myotis lucifugus	ENSMLUG00000002627	2 retrocopies	retro_mluc_1179, retro_mluc_663,
Mus musculus	ENSMUSG00000020993	2 retrocopies	retro_mmus_1734, retro_mmus_2069,
Oryctolagus cuniculus	ENSOCUG00000002171	1 retrocopy	retro_ocun_813,
Sarcophilus harrisii	ENSSHAG00000001400	1 retrocopy	retro_shar_235,
Ictidomys tridecemlineatus	ENSSTOG00000002897	2 retrocopies	retro_itri_476, retro_itri_795 ,
Tupaia belangeri	ENSTBEG00000003331	1 retrocopy	retro_tbel_4529,