RetrogeneDB ID: retro_itri_1903

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH398893.1:1..739(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000022929
• Aliases: None
• Description: None

Sequence

>retro_itri_1903
TTGGAGATCTCATTCACATCTGCATGTATTCCCAGATACTTATATAACATAGCAACAGGTGACAAGATGATTACCTACAA
TGCCTGTGTCAGCCAAGTATTTTTTACTGACCTCTTTGGTGTAACTGAATTTTTTCTCCTTGCTGCCATGTCCTATGATC
GCTATGTGGCCATCTGCAAGCCCCTGCATTATGTGACTATCATGAGTAGTAGAGTCTGCAGGAGACTTGTGTTTTGTTGT
TGGGTAGCAGGTCTGTTTATTTTAACCCCCCCACTGAGCCTAGGCCTGAATCTGGAGTTTTGTGATTCTAATATCATTGA
TCATTTTGTTTGTGATGCATTTCCCCTCCTGAAAATCTCTTGTTCAAATACTTGGTTTATGGAACAGACCATTATCATCT
GTGCTGTACTGACCCTCATTTTGACACTCATGTGCGTAGTGCTGTCCTACATTTATATCATCAAGACAATTTTAAGATTT
CCTTCTGCTCAGCAAAAGAAAAAAGCCTTTTCTACCTGTTCTTCCCATATGATTGTGGTTTCTCTCACCTATGGCAGCTG
CATCTTCATCTACATTAAACCTTCAGCAAAGGACTCAGTGGCCATAAATAAGGGGGTGACTGTCCTCACCACTTCTATGG
CTCCCATGCTGAACCCTTTCATTTACACACTAAGGAACAAGCAAGTACAACAGGCCTTCAAGGACTCAGTCAAAAGAATT
GTAATATTTTCCAAGAAA

Alignment

ORF - retro_itri_1903 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.27 %
• Parental protein coverage: 78.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEVSFTTVCIPRFLYTLSTGDNTVTYNACATQIFFVFLFGATEFFLLAAMSYDRYVAIIKCRYLEYSAVS
          LE.SFT..CIPR.LY...TGD...TYNAC..Q.FF..LFG.TEFFLLAAMSYDRYVAI..C..L.Y....
Retrocopy LEISFTSACIPRYLYNIATGDKMITYNACVSQVFFTDLFGVTEFFLLAAMSYDRYVAI--CKPLHYVTIM

Parental  PSSYCKRILFCCWVAGLFILIPPLSLGLNLEFCDSNIIDHFVCDASPLLKISCSNTWFMEQTIIICAVLT
          .S..C.R..FCCWVAGLFIL.PPLSLGLNLEFCDSNIIDHFVCDA.PLLKISCSNTWFMEQTIIICAVLT
Retrocopy SSRVCRRLVFCCWVAGLFILTPPLSLGLNLEFCDSNIIDHFVCDAFPLLKISCSNTWFMEQTIIICAVLT

Parental  FIMTLMCVVLSYIYIIKTILRFPSAKQKKKAFSTCSSHMIVVSLTYGSCIFIYIKPSAKDSVAINKRVTV
          .I.TLMCVVLSYIYIIKTILRFPSA.QKKKAFSTCSSHMIVVSLTYGSCIFIYIKPSAKDSVAINK.VTV
Retrocopy LILTLMCVVLSYIYIIKTILRFPSAQQKKKAFSTCSSHMIVVSLTYGSCIFIYIKPSAKDSVAINKGVTV

Parental  LTTSIAPMLNPFIYTLRNKQVKQAFKDSVKRIVIFSKK
          LTTS.APMLNPFIYTLRNKQV.QAFKDSVKRIVIFSKK
Retrocopy LTTSMAPMLNPFIYTLRNKQVQQAFKDSVKRIVIFSKK

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_1903 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1903 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000022929	1 retrocopy	retro_itri_1903 ,