RetrogeneDB ID: retro_itri_229

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393280.1:31183542..31184583(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB2
• Ensembl ID: ENSSTOG00000001275
• Aliases: None
• Description: cyclin B2 [Source:HGNC Symbol;Acc:1580]

Sequence

>retro_itri_229
AAAACTCAAAACACCAAAGTATCAGTTCAGCCCACCAAAGCAACAAATATCAACAAACAACTGAAACCCACTGCTTCTGT
GAAACCAGTACAGATGGAAATGTTGGCTCCAAAGGGTCCTTCTCCCACACCTGAGGATGTCTCCATGAAGGAAGAGAACC
TCTGCCAAGCTTTCTCTGATGCCTTGCTCTGCAAAATTGAGGACATTGATAATGAGGATTGGGAGAACCCTCAGTTCTGC
AGTGACTATGTTAAAGATATCTACCAGTATCTAAGACAGCTTGAGGTTTTGCAATCCATAAACCCACATTTCTTGGATGG
AAGAGATATAAATGGACGTATGAGTGCCATCCCAATGCACTGGCTGGTTCAAGTCCACCCCAAGTTTAGGCTTCTGCAGG
AAACTCTGTACATGTGCATTGCTGTCATGGATCGATTTTTACAGGTTCAGCCAGTCTCCCATAAGAAACTTCAGTTGGTT
GAGATTTCAACTCTGCTCTTGCCTTCCAAGTATGAGGAGATGTTTTCTCCAAATATAGAAGACTTCGTCTACATCACAGA
CGATGCTTATACCAGTTCTCAAATCCGAGAAATGGAAACTCTAATTTTGAAAGAACTGAAGTTTGAGTTGAGTCAACCCT
TGCCACTTCACTTTTTAAGGTGAGCATCAAAAGCTGGGGAAGTTGATGTTGAACGGCACACATTAGCCAAATATTTGATG
GAGCTGACTCTCATTGATTATGACATGGTGCATTATCACCCTTCTAAGGTAGCTGCAGCTGCTTCCTGCTTGTCTCAGAA
GGTTCTAGGCCAAGGAAAATGGAACTTAAATCAGCAGTATTACACAGGATACACAGGGAATGAAGTATTGGAAGTCATGC
AGCACATGGCCAAAAATGTGGTGAAAGTAAATGAAAACTTAACTAAATTCATCGCCATCAAGAATAAGTATGCCAGCAGC
AAACTCCTGAAGATCAGCACGATCCCTCAGCTGAACTCCAAAACCATCAAATACCATGCCTCCCCTCTGATGGAGAGGTC
C

Alignment

ORF - retro_itri_229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.95 %
• Parental protein coverage: 87.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTQNTKVSVQPTKATNVNKQLKPTASVKPVQMEMLAPKGPSPTPEDVSMKEENLCQAFSDALLCKIEDID
          KTQNTKVSVQPTKATN.NKQLKPTASVKPVQMEMLAPKGPSPTPEDVSMKEENLCQAFSDALLCKIEDID
Retrocopy KTQNTKVSVQPTKATNINKQLKPTASVKPVQMEMLAPKGPSPTPEDVSMKEENLCQAFSDALLCKIEDID

Parental  NEDWENPQLCSDYVKDIYQYLRQLEVLQSINPHFLDGRDINGRMRAILVDWLVQVHSKFRLLQETLYMCI
          NEDWENPQ.CSDYVKDIYQYLRQLEVLQSINPHFLDGRDINGRM.AI...WLVQVH.KFRLLQETLYMCI
Retrocopy NEDWENPQFCSDYVKDIYQYLRQLEVLQSINPHFLDGRDINGRMSAIPMHWLVQVHPKFRLLQETLYMCI

Parental  AVMDRFLQVQPVSRKKLQLVGITALLLASKYEEMFSPNIEDFVYITDNAYTSSQIREMETLILKELKFEL
          AVMDRFLQVQPVS.KKLQLV.I..LLL.SKYEEMFSPNIEDFVYITD.AYTSSQIREMETLILKELKFEL
Retrocopy AVMDRFLQVQPVSHKKLQLVEISTLLLPSKYEEMFSPNIEDFVYITDDAYTSSQIREMETLILKELKFEL

Parental  GRPLPLHFLRRASKAGEVDVEQHTLAKYLMELTLIDYDMVHYHPSKVAAAASCLSQKVLGQGKWNLKQQY
          ..PLPLHFLR.ASKAGEVDVE.HTLAKYLMELTLIDYDMVHYHPSKVAAAASCLSQKVLGQGKWNL.QQY
Retrocopy SQPLPLHFLR*ASKAGEVDVERHTLAKYLMELTLIDYDMVHYHPSKVAAAASCLSQKVLGQGKWNLNQQY

Parental  YTGYTENEVLEVMQHMAKNVVKVNENLTKFIAIKNKYASSKLLKISTIPQLNSKTIKDLASPLMERS
          YTGYT.NEVLEVMQHMAKNVVKVNENLTKFIAIKNKYASSKLLKISTIPQLNSKTIK..ASPLMERS
Retrocopy YTGYTGNEVLEVMQHMAKNVVKVNENLTKFIAIKNKYASSKLLKISTIPQLNSKTIKYHASPLMERS

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_229 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_229 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005269	1 retrocopy	retro_btau_1584,
Homo sapiens	ENSG00000157456	1 retrocopy	retro_hsap_3816,
Nomascus leucogenys	ENSNLEG00000011543	1 retrocopy	retro_nleu_212,
Otolemur garnettii	ENSOGAG00000012885	2 retrocopies	retro_ogar_1770, retro_ogar_2766,
Pongo abelii	ENSPPYG00000006517	2 retrocopies	retro_pabe_3073, retro_pabe_3074,
Pan troglodytes	ENSPTRG00000007123	1 retrocopy	retro_ptro_2597,
Ictidomys tridecemlineatus	ENSSTOG00000001275	1 retrocopy	retro_itri_229 ,
Tarsius syrichta	ENSTSYG00000013818	1 retrocopy	retro_tsyr_1402,