RetrogeneDB ID: retro_itri_1590

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393561.1:1851915..1852437(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019959
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNB1IP1
• Ensembl ID: ENSSTOG00000004394
• Aliases: None
• Description: cyclin B1 interacting protein 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:19437]

Sequence

>retro_itri_1590
ATGTCTTTGTGTGAAGATATGTTGTTTTGTAATTATCGAAAGTGTCACATCAAACTCTCTGGTTATGCCTGGGTCACTGC
CTGTTCTCATATCTTCTGTGATCAGCATGGCAGTGGTGAATTTAGTTGTTCACCAGCTATCTGCCCTGCCTGCAACAGTA
CCCTTTCTGGAAAGCTGGATATTGTCTGCACTGAACTCAGTCCTTCAGAGGAATATAAAGCTATGGTGTTGGCAGGGCTG
CCACCAGAGATTGTGTTAGACATTAGCTCCCGAGCACTGGTTTTCTGGACATATCAGGTACATCAGGAACGTCTCTATCA
AGAATATAATTTTAGCAAGGCTGAGGGTCATCTGAAACAGATGGAGACAATATATACTCAGCAAATACAGAGCAAAGATG
TAGAATTGACCTCTATGAAAGGGAAGGTCACCTCTATGAAGAAAGTGCTAGAAGAATACAAGAAAAAGTTCAGTGACATC
CCAGAGAAACGTATGGAGCATAATAGTCAGTATCAAAAGCTC

Alignment

ORF - retro_itri_1590 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68. %
• Parental protein coverage: 64.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLCEDMLLCNYRKCRIKLSGYAWVTACSHIFCDQHGSGEFSRSPAICPACNSTLSGKLDIVRTELSPSE
          MSLCEDML.CNYRKC.IKLSGYAWVTACSHIFCDQHGSGEFS.SPAICPACNSTLSGKLDIV.TELSPSE
Retrocopy MSLCEDMLFCNYRKCHIKLSGYAWVTACSHIFCDQHGSGEFSCSPAICPACNSTLSGKLDIVCTELSPSE

Parental  EYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKLQCKLKITYILLTVCILQEDLVLVSFT
          EYKAMVLAGL.PEIVLDISSRAL.FWTYQVHQERLYQEYNFSK....LK......T..I...D..L.S..
Retrocopy EYKAMVLAGLPPEIVLDISSRALVFWTYQVHQERLYQEYNFSKAEGHLKQMETIYTQQIQSKDVELTSMK

Parental  CQYWSHSSQIIDDTNFLLGTLPNKYLTFTYLYCNL
          ....S................P.K.......Y..L
Retrocopy GKVTS-MKKVLEEYKKKFSDIPEKRMEHNSQYQKL

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_1590 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1590 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009967	2 retrocopies	retro_cjac_3244, retro_cjac_4197,
Homo sapiens	ENSG00000100814	1 retrocopy	retro_hsap_4877,
Gorilla gorilla	ENSGGOG00000004586	1 retrocopy	retro_ggor_3046,
Microcebus murinus	ENSMICG00000000893	2 retrocopies	retro_mmur_1264, retro_mmur_1551,
Macaca mulatta	ENSMMUG00000016251	2 retrocopies	retro_mmul_2617, retro_mmul_371,
Nomascus leucogenys	ENSNLEG00000010636	1 retrocopy	retro_nleu_2556,
Pan troglodytes	ENSPTRG00000006088	1 retrocopy	retro_ptro_3249,
Rattus norvegicus	ENSRNOG00000026056	1 retrocopy	retro_rnor_842,
Ictidomys tridecemlineatus	ENSSTOG00000004394	1 retrocopy	retro_itri_1590 ,