RetrogeneDB ID: retro_itri_258

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:4032876..4033365(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSSTOG00000010560
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_itri_258
ACAGCTCTTTTTTACTATCTTCCTCTCACTGCCTTGGTGGATGGGCAGATCTTCTGTCTACATGGTGACCTCTCACCATC
CATAGACACACTGGATCATATCAGAGCTTTTGATCGTCTACAAGAAGTTCCCCATGAGGGTCCAATGTGTGACTTGCTGT
GGTCAGATCCAGATGATCGTGGTAGTTGGGGTATATCTCCTTGAGGAGCTGGTTACACATTTGGAAAAGATATTTCTGAG
ACATTTAATCATGCCAATGGCCTCACATTAGTGTCTAGAGCTCACCAGCTGGTGATGGAGGGATATAACTGGTGCCATGA
TCGGAATGTAGTAACAATTTTCAGTGCTCCAAACTATTGTTATCATTGCGGTTACCACGCTGCAATCATGGAACTTGATG
ATACTCTAAAATATTCTTTCTTGCAGTTTGATCCATTACCTCCTAGAGGCGAACCACATGTTACTGGTCATACCCCAGAC
TACTTCCTG

Alignment

ORF - retro_itri_258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.41 %
• Parental protein coverage: 52.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGA
          T.LF.YLPLTALVDGQIFCLHG.LSPSIDTLDHIRA.DRLQEVPHEGPMCDLLWSDPDDRG.WGISP.GA
Retrocopy TALFYYLPLTALVDGQIFCLHGDLSPSIDTLDHIRAFDRLQEVPHEGPMCDLLWSDPDDRGSWGISP*GA

Parental  GYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSF
          GYTFG.DISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCY.CG..AAIMELDDTLKYSF
Retrocopy GYTFGKDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYHCGYHAAIMELDDTLKYSF

Parental  LQFDPAPRRGEPHVTRRTPDYFL
          LQFDP.P.RGEPHVT..TPDYFL
Retrocopy LQFDPLPPRGEPHVTGHTPDYFL

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_258 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_258 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Callithrix jacchus	ENSCJAG00000013634	2 retrocopies	retro_cjac_1346, retro_cjac_4113,
Homo sapiens	ENSG00000113575	1 retrocopy	retro_hsap_369,
Nomascus leucogenys	ENSNLEG00000026729	1 retrocopy	retro_nleu_2441,
Otolemur garnettii	ENSOGAG00000009695	2 retrocopies	retro_ogar_3414, retro_ogar_921,
Rattus norvegicus	ENSRNOG00000005389	5 retrocopies	retro_rnor_1263, retro_rnor_1264, retro_rnor_1265, retro_rnor_1266, retro_rnor_817,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Ictidomys tridecemlineatus	ENSSTOG00000010560	1 retrocopy	retro_itri_258 ,