RetrogeneDB ID: retro_itri_1891

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH395213.1:12499..13282(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000025706
• Aliases: None
• Description: None

Sequence

>retro_itri_1891
CTCCTCAAGCCGCTCTTCCCCACCTGCCCCATGCAGGAGGAGACCGCCAAGCTCGTGGCCTGCCTCTGCGTGCTGCTGCT
CACGGCGGTGAACTGCTACAGCGTGAAAGCTGCCACCTGCGTGCAGGACGCCTTAGCGGCAGGCAAGCTCCTGCCCTGGC
CCTGATCATCCTGCTTGGCTTCATCCAGATCCGGAAGGGTGGGTGGCGTGTCTAATCTGAACCCAGAGTTCTCCTTCCAA
GGCACCAACCTGGACGTGGGCAACATCGTGCTGGCCTTGTACAGTGGCCTCTTTGCCTACGGAGGATGGAATTACCTGAA
CTTTGTCACAGAGGAGATGATCAACCCCTACAGGAACCTGGCCCTGGCCATCATCATCTCCCTCCCCATCGTCACCCTGG
TGTACGTGCTGACGAACCTGGCCTACTTCACCACACTGACCACTGAGCAGATGCTGACATCCGAGGCTGTGGCCTTGGAC
TTTGGGAACTACCACCTGGGAGTCATGTCCTGGATCATCCCCGTCTTTGTGGGCCTGTCCTGCTTCGGCTCTGTCAACGG
GTTCCTGTTCACATCCTCCAGGCTGTTCTTCGTGGGGTCCAGGGAAGGCCACCTGCCCTCGATCCTGTCCATGATCCACC
CACAGCTCCTGACACCCATGCCATCCCTTGTGTTCACGTGCATCATGACCCTGCTGTATGCCTTCTCCAAAGACATCTTC
TCCGTCATCAACTTCTTCAGCTTCTTCAACTGGCTCTGTGTGGCCCTGGCCATCATGGGTATG

Alignment

ORF - retro_itri_1891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.36 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLKPLFPTCPVPEEAAKLVACLCVLLLTAVNCYSVKAATRVQDAFAAAKLL-ALALIILLGFIQI-GK-G
          LLKPLFPTCP..EE.AKLVACLCVLLLTAVNCYSVKAAT.VQDA.AA.KLL.ALALIILLGFIQI.G..G
Retrocopy LLKPLFPTCPMQEETAKLVACLCVLLLTAVNCYSVKAATCVQDALAAGKLL<ALALIILLGFIQI>GRVG

Parental  GVSNLNPEFSFQGTNLDVGNIVLALYSGLFAYGGWGTRRAVLQQPVPPCCRNLPLAIIISLPIVTLVYVL
          GVSNLNPEFSFQGTNLDVGNIVLALYSGLFAYGGW.....V......P..RNL.LAIIISLPIVTLVYVL
Retrocopy GVSNLNPEFSFQGTNLDVGNIVLALYSGLFAYGGWNYLNFVTEEMINPY-RNLALAIIISLPIVTLVYVL

Parental  TNLAYFTTLTTEQMLTSEAVAVDFGNYHLGVMSWIIPVFVGLSCFGSVNGSLFTSSRLFFVGSREGHLPS
          TNLAYFTTLTTEQMLTSEAVA.DFGNYHLGVMSWIIPVFVGLSCFGSVNG.LFTSSRLFFVGSREGHLPS
Retrocopy TNLAYFTTLTTEQMLTSEAVALDFGNYHLGVMSWIIPVFVGLSCFGSVNGFLFTSSRLFFVGSREGHLPS

Parental  ILSMIHPQLLTPMPSLVFTCIMTLLYAFSKDIFSVINFFSFFNWLCVALAIIGM
          ILSMIHPQLLTPMPSLVFTCIMTLLYAFSKDIFSV.........LCVALAI.GM
Retrocopy ILSMIHPQLLTPMPSLVFTCIMTLLYAFSKDIFSVXXXXXXXXXLCVALAIMGM

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_1891 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1891 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000004455	1 retrocopy	retro_csav_1,
Ictidomys tridecemlineatus	ENSSTOG00000025706	1 retrocopy	retro_itri_1891 ,