RetrogeneDB ID: retro_itri_1769

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393740.1:354871..355387(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2A2
• Ensembl ID: ENSSTOG00000003538
• Aliases: None
• Description: casein kinase 2, alpha prime polypeptide [Source:HGNC Symbol;Acc:2459]

Sequence

>retro_itri_1769
GGACTGGGTCCTGGTGAAGTTCCCTCACCCTGCTCAGGAGTACAATGTACTTCAAGGTACTTCAAGGGACCAGAGCTTCT
TGTGGACTGTCAGATACATGATGACAGCTGGGACATGTGGAGTTTGAGCTGTATGTTGGCAAGCGTGGTATTTCAAAAGG
AACCCTTCTTCCACAGACAGGGCAGCTGTGGCCAGCTTGTTCGCATCGCCAAGGTTCTGGGTACAGATGAGCTGTGTAGG
TATCTGAAGAAGTATCATATAGACTCAGATCCACGTCTCAAAGATATCCTGGGACATCATTCACAGAAACGCTGGGAAAA
CTTTATGCGTACTGAGAACAGGCACCTTGTTAGCCCTGAAGCCAGAGATCTTTGGGATAAACTCCCACAATATGACCATC
AACAGACACTGACTGCCAAAGGAGTCATGAAGCTCCGGTACTTCTACCCGACGGTGAAGGAGCAGTCCCAGCCTTGGGCA
GAGAATGCTGTGCTTTCCAGTGGTCTCACGGCAGCC

Alignment

ORF - retro_itri_1769 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.93 %
• Parental protein coverage: 52.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGQDNYDQLVRIA
          GL.....P.....V...SRYFKGPELLVD.Q..D.S.DMWSL.CMLAS..F.KEPFFH.Q....QLVRIA
Retrocopy GLGPGEVPSPCSGVQCTSRYFKGPELLVDCQIHDDSWDMWSLSCMLASVVFQKEPFFHRQGSCGQLVRIA

Parental  KVLGTDELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAK
          KVLGTDEL..YLKKYHID.DP...DILG.HS.KRWENF...ENRHLVSPEA.DL.DKL..YDHQQ.LTAK
Retrocopy KVLGTDELCRYLKKYHIDSDPRLKDILGHHSQKRWENFMRTENRHLVSPEARDLWDKLPQYDHQQTLTAK

Parental  EAMEHPYFYPVVKEQSQPCAENAVLSSGLTAA
          ..M...YFYP.VKEQSQP.AENAVLSSGLTAA
Retrocopy GVMKLRYFYPTVKEQSQPWAENAVLSSGLTAA

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_1769 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1769 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000000930	1 retrocopy	retro_eeur_442,
Macropus eugenii	ENSMEUG00000013416	1 retrocopy	retro_meug_1470,
Myotis lucifugus	ENSMLUG00000000283	2 retrocopies	retro_mluc_1999, retro_mluc_2562,
Mustela putorius furo	ENSMPUG00000004713	1 retrocopy	retro_mputfur_1121,
Ochotona princeps	ENSOPRG00000011847	2 retrocopies	retro_opri_149, retro_opri_723,
Ictidomys tridecemlineatus	ENSSTOG00000003538	1 retrocopy	retro_itri_1769 ,