RetrogeneDB ID: retro_itri_937

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393346.1:8273230..8273587(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YPEL2
• Ensembl ID: ENSSTOG00000001013
• Aliases: None
• Description: yippee-like 2 (Drosophila) [Source:HGNC Symbol;Acc:18326]

Sequence

>retro_itri_937
GTGAAGATGACAAGATTCAAGAGTTTCCAGGCATGTCTGCTCCTCTGTCACAGGATCTACAGCTGCACTCACTGTAGCGC
TCACATGGCCAATCACGATGGACGGCTTTCCAAGCCATTCCGAGGAAGTCAAAGAGGAGCATGCCTCTTTAACTTAGTAG
TTAACATGGGCTGTGGGCCTGCAGAAGAGCAAGTGTCACAAACAGGATGGCATACAGTTGCAGACATTTACTGTCAAAAC
TGCAAAACCACCCTGGGGGGCTGAAAATATGAACATGCTTTTGAAAACAACCAGAAATCCAAAGAAGACAAATACAACAT
TCAGCTAGCACACATGATCAAGAACAGTGGCTGGGAC

Alignment

ORF - retro_itri_937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 99.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKMTRSKTFQAYLPSCHRTYSCIHCRAHLANHDELISKSFQGSQGRAYLFNSVVNVGCGPAEERVLLTGL
          VKMTR.K.FQA.L..CHR.YSC.HC.AH.ANHD...SK.F.GSQ..A.LFN.VVN.GCGPAEE.V..TG.
Retrocopy VKMTRFKSFQACLLLCHRIYSCTHCSAHMANHDGRLSKPFRGSQRGACLFNLVVNMGCGPAEEQVSQTGW

Parental  HAVADIYCENCKTTLGW-KYEHAFESSQKYKEGKYIIELAHMIKDNGWD
          H.VADIYC.NCKTTLG..KYEHAFE..QK.KE.KY.I.LAHMIK..GWD
Retrocopy HTVADIYCQNCKTTLGG*KYEHAFENNQKSKEDKYNIQLAHMIKNSGWD

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_937 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_937 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000018575	1 retrocopy	retro_ecab_616,
Otolemur garnettii	ENSOGAG00000029581	1 retrocopy	retro_ogar_1226,
Sorex araneus	ENSSARG00000009791	2 retrocopies	retro_sara_318, retro_sara_650,
Ictidomys tridecemlineatus	ENSSTOG00000001013	1 retrocopy	retro_itri_937 ,
Tupaia belangeri	ENSTBEG00000013138	1 retrocopy	retro_tbel_808,
Tarsius syrichta	ENSTSYG00000005518	1 retrocopy	retro_tsyr_2143,
Vicugna pacos	ENSVPAG00000000381	1 retrocopy	retro_vpac_128,