RetrogeneDB ID: retro_itri_1618

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393576.1:505661..506541(-)
• Located in intron of: ENSSTOG00000027659

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CB
• Ensembl ID: ENSSTOG00000029081
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9282]

Sequence

>retro_itri_1618
CTGGTGGTACCAGGATGTCGTCCAGGAAAGATTGTGCAGATGACTCAAGCAGAAGTCCAGGGCTTATGTATCAAGTCTCA
TGCAATCTTCCTCAGCCAGCCTATTCTTTTGGAATTGGAAGCACCACTGAAAATTTGTGGAGATATTCATGGACAGTATA
CAGATTTACTGAGATTATTTGAATATGGAGGTTTCCCACCAGAAGCCAACTATCTTTTCTTAGGAGATTATGTGGAGAGA
GGAACGCAGTCTTTGGAAACCATTTGTTTGCTATTGGCTTATAAAATCAAATATCCAGAGAACTTCTTTCTCTTAAGAGG
AAATCATGAAATGTGCTAGCATCGATCGCATTTATGGATTCTATGATGAATGCAAACGAAGGTTTAATATTAGACTGTGG
AAGACCTTCACTGATTGTTTTGACTGTCTGCCTATAGCTGCCATTGTGGATGAGAAGATCTTCTGTCGCCACGGAGGACT
ATCACCAGACTTGCAATCTATGGAGCAGATTCAGAGAATTATGAGACCCACTAATGTCCCTGATGCAGGTTTACTCTGTG
ATCTGCTGTGATCTGACCCAGATAAGGATGTGCAAGGCTGGGGAGAAAATGATCGTGGTGTTTCCTTTACTTTTGGAGCT
GAGGTAGTCAGTGAATTTCTGAATCATCATGATTTAGACTTGATTTGTCGAGCTCATCAGGTGGTGGGAGATGGATATGA
ATTTTTTGCTAAACGACAATTGGTAACCCTATTTTCAGCCCCAAATTACTGTGGCGAGTTTGACAATGCTGGTGGAATGA
TGAGTGTGGATGAAACTTTGATGTGTTCATTTCAGATATTGAAACCATCTGAAAAGAAAGCTAAGTACCAGTATGGTGGA

Alignment

ORF - retro_itri_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 93.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSVRGCRPGKIVQMTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQYTDLLRLFEYGGFPPEAN
          L.V.GCRPGKIVQMT.AEV.GLCIKS..IFLSQPILLELEAPLKICGDIHGQYTDLLRLFEYGGFPPEAN
Retrocopy LVVPGCRPGKIVQMTQAEVQGLCIKSHAIFLSQPILLELEAPLKICGDIHGQYTDLLRLFEYGGFPPEAN

Parental  YLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHE-CASINRIYGFYDECKRRFNIKLWKTFTDC
          YLFLGDYV.RG.QSLETICLLLAYKIKYPENFFLLRGNHE.CASI.RIYGFYDECKRRFNI.LWKTFTDC
Retrocopy YLFLGDYVERGTQSLETICLLLAYKIKYPENFFLLRGNHE>CASIDRIYGFYDECKRRFNIRLWKTFTDC

Parental  FNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWSDPDKDVQGWGENDRGVSF
          F.CLPIAAIVDEKIFC.HGGLSPDLQSMEQI.RIMRPT.VPD.GLLCDLL.SDPDKDVQGWGENDRGVSF
Retrocopy FDCLPIAAIVDEKIFCRHGGLSPDLQSMEQIQRIMRPTNVPDAGLLCDLL*SDPDKDVQGWGENDRGVSF

Parental  TFGADVVSKFLNRHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGGMMSVDETLMCSFQI
          TFGA.VVS.FLN.HDLDLICRAHQVV.DGYEFFAKRQLVTLFSAPNYCGEFDNAGGMMSVDETLMCSFQI
Retrocopy TFGAEVVSEFLNHHDLDLICRAHQVVGDGYEFFAKRQLVTLFSAPNYCGEFDNAGGMMSVDETLMCSFQI

Parental  LKPSEKKAKYQYGG
          LKPSEKKAKYQYGG
Retrocopy LKPSEKKAKYQYGG

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_1618 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1618 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000004612	2 retrocopies	retro_rnor_1455, retro_rnor_2344,
Ictidomys tridecemlineatus	ENSSTOG00000029081	2 retrocopies	retro_itri_1200, retro_itri_1618 ,