RetrogeneDB ID: retro_itri_1890

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH395041.1:12034..12449(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000028527
• Aliases: None
• Description: None

Sequence

>retro_itri_1890
TTTGCCATTTTCTACAGCAGACCAAAAAAGTAATTAAATAGACATTTTTTCCTCATAGGCAATAAACTTGAACATGAGGA
CTTCTATGCAGACTTCAAACTATTCAATTCAGAAATGGTTTACAGATAATTTTGCAACAAAAATAAGAAATTAAACTGCA
TTACAAGAATAAGGAGGAGAATTATTCATTTTACTAGCTCTGATCAGAGGAAGGCTACTGCTGCTTTCTTTGTCATATGG
GATATGGTTCTATATTTGGGAGAAGTCCAGAAAATGCACATAAAATATCAATCTATGGAAATACATCCTCTAATCCTTTC
AGAGTTGCTGCCTATGGAAGTTTCAACTTTTATATTACTTTCTTGACTGTTCTCAAATAATGAAGAAGGCAACACATTAT
GGCTTCTTAAATTTC

Alignment

ORF - retro_itri_1890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.68 %
• Parental protein coverage: 88.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FAILYSRPKSASNEHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMIRKKIIHFTGSDQR
          FAI.YSRPK...N.H.F.I.N.LE.E.FYADF...N..MVYR..C..NKKL..IT.IR..IIHFT.SDQR
Retrocopy FAIFYSRPKK*LNRHFFLIGNKLEHEDFYADFKLFNSEMVYR*FCNKNKKLNCITRIRRRIIHFTSSDQR

Parental  KQANAAFLVGCYMVIYL-GRTPEDAYRILIFGDTSYIPFRDAAYGSCNFYIT-LLDCFHAVKKAMQYGFL
          K.A.AAF.V...MV.YL.GR.PE.A..I.I.G.TS..PFR.AAYGS.NFYIT..LDC....KKA..YGFL
Retrocopy K-ATAAFFVIWDMVLYL<GRSPENAHKISIYGNTSSNPFRVAAYGSFNFYIT<FLDCSQIMKKATHYGFL

Parental  NF
          NF
Retrocopy NF

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_1890 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1890 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000081377	2 retrocopies	retro_hsap_3729, retro_hsap_3845,
Macaca mulatta	ENSMMUG00000005997	1 retrocopy	retro_mmul_1615,
Nomascus leucogenys	ENSNLEG00000016822	1 retrocopy	retro_nleu_1981,
Pongo abelii	ENSPPYG00000019417	1 retrocopy	retro_pabe_208,
Pan troglodytes	ENSPTRG00000021155	2 retrocopies	retro_ptro_2524, retro_ptro_2621,
Ictidomys tridecemlineatus	ENSSTOG00000027626	1 retrocopy	retro_itri_1825,
Ictidomys tridecemlineatus	ENSSTOG00000028527	3 retrocopies	retro_itri_1798, retro_itri_1821, retro_itri_1890 ,