RetrogeneDB ID: retro_itri_1195

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393397.1:2609612..2609985(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000010256
• Aliases: None
• Description: None

Sequence

>retro_itri_1195
ATCCCTCACAGTACCAAACAATTCCCTGGGTATGATTCTGAAAACAAGGAGTTTAGTGCAGAAGTACATCAGAAACACAT
CAGGGGTCAGAATGTTGCAGATGACATGCATTATCTAATGGAGGAAGGTGAAGATGTTTACAAGAAACAATTCTCTCAGT
ACATACAGAACAAAGTTACTCCAGACACAATGAAGGAGATTTATAAGAAAGCTCCTTCTACTATATGAGAGAATCCAGTC
TATGAGCAGAAACCCAAGAGAAGTTAATAAGAAGAGGTGGAAACATTCCCAAATGTCCTTTCCATAGAGGAAAGATCAGA
TGGCCCAAAAGAAGGTGAGCTTCCTCAGAGGTCAGGAATGGGCTGCTGTGAGC

Alignment

ORF - retro_itri_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.05 %
• Parental protein coverage: 54.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRHFTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
          I.H.TK.FPGYDSE.KEF.AEVH.KHI.GQNVAD.M.YLMEE.ED.YKKQFSQYI.N.VTPD.M.E.YKK
Retrocopy IPHSTKQFPGYDSENKEFSAEVHQKHIRGQNVADDMHYLMEEGEDVYKKQFSQYIQNKVTPDTMKEIYKK

Parental  AHSAIRENPVYEKKPKRE-VKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
          A.S.I.ENPVYE.KPKR...KK..W....MS....KD..AQKK.SFLR.QE.AA.S
Retrocopy APSTI*ENPVYEQKPKRS>NKKR-WKHSQMSFP*RKDQMAQKKVSFLRGQEWAAVS

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_1195 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1195 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,
Ictidomys tridecemlineatus	ENSSTOG00000010256	2 retrocopies	retro_itri_1195 , retro_itri_721,