RetrogeneDB ID: retro_itri_1200

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393399.1:5231531..5232450(+)
• Located in intron of: None

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_1200
GGATGTTGTCCAGGAAAGATTGTGCAGTTGACTGAAGCAGAAGTTCAGGGCTTATGTATCAATCTCATGAAATCTTGCTC
AGCCAGCCTATTCTTTTGGAATTAGAAGTACCACTGAAAATTTGTGGAGATATTCATGGACAGTATATAGATTTACTGAG
ATTATTTGAATATGGAAGTTTCCCACCAGAAGCCAATCTGTTTTATTCGGAAATTATGTGGACAGAGGAAAGCAGTCTTT
GGAAACCATTTGTTTGCTATTGGCTTATAAAATCAAATATCCAGAGAACTTCTTTCTCTCAAGAGAAAATTATGAATGTG
CTATCATCAAATGCATTTATGGATTCTATGATGAATGCAAATGAAGGTTTAATCTTAAGTTGTGGAAGACCTTCACCGGT
TGCTTTAACTCTCTGCCTATAGCTGCCATTGTGGATGAGAAGATCTTCTGTTTTATGGAGGACTATCACCAGACTTGCAA
TATATGGAGCAGATTTGGAGAATAATAGGACCCACAGATATCCCTGATATAGGTTTGCTCTGTGATTTTCTGTGGTCTGA
CCCAGATAAGGATGTGCAAGGCTGGGGAGAAAACTGATCATAGTGTTTCCTTTGCTTTTGGAGCTGATGAATTCAGTAAA
TTTCTGAATCATCATGATTTAGACTTGATTTGTCGAGCCCATCAGGTGGTGGAAGATGGATATGAATTTTTTGCAAAATG
ACAATTGATCACCCTATTTTCAGCCCCACATTACTGTGGCAAGTTTGATAATACTGGTAGAATGATGAATGTGGATGAAA
CTTTGATATGCTCATTTCAGATATTGAAATCATCTGAAATGAAAACTAAGTATCAGTATGGTGGACTGAATTCTGGATGT
CCTGTCACTCTACCTCAAATAGATAATCCACTGAAAAAA

Alignment

ORF - retro_itri_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.71 %
• Parental protein coverage: 98.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GCRPGKIVQMTEAEVRGLCI-KSREIFLSQPILLELEAPLKICGDIHGQYTDLLRLFEYGGFPPEANYLF
          GC.PGKIVQ.TEAEV.GLCI..S.EI.LSQPILLELE.PLKICGDIHGQY.DLLRLFEYG.FPPEAN...
Retrocopy GCCPGKIVQLTEAEVQGLCI<QSHEILLSQPILLELEVPLKICGDIHGQYIDLLRLFEYGSFPPEANLFY

Parental  -LGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRFNIKLWKTFTDCFNC
          ..G.YVDRGKQSLETICLLLAYKIKYPENFFL.R.N.ECA.I..IYGFYDECK.RFN.KLWKTFT.CFN.
Retrocopy <FGNYVDRGKQSLETICLLLAYKIKYPENFFLSRENYECAIIKCIYGFYDECK*RFNLKLWKTFTGCFNS

Parental  LPIAAIVDEKIFCC-HGGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWSDPDKDVQGWGEN-DRGVSFT
          LPIAAIVDEKIFC...GGLSPDLQ.MEQI.RI..PTD.PD.GLLCD.LWSDPDKDVQGWGEN.D..VSF.
Retrocopy LPIAAIVDEKIFCF<YGGLSPDLQYMEQIWRIIGPTDIPDIGLLCDFLWSDPDKDVQGWGEN>DHSVSFA

Parental  FGADVVSKFLNRHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGGMMSVDETLMCSFQIL
          FGAD..SKFLN.HDLDLICRAHQVVEDGYEFFAK.QL.TLFSAP.YCG.FDN.G.MM.VDETL.CSFQIL
Retrocopy FGADEFSKFLNHHDLDLICRAHQVVEDGYEFFAK*QLITLFSAPHYCGKFDNTGRMMNVDETLICSFQIL

Parental  KPSEKKAKYQYGGLNSGRPVTPPRTANPPKK
          K.SE.K.KYQYGGLNSG.PVT.P...NP.KK
Retrocopy KSSEMKTKYQYGGLNSGCPVTLPQIDNPLKK

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_1200 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1200 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,