RetrogeneDB ID: retro_itri_381

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393288.1:6459122..6460094(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R2D
• Ensembl ID: ENSSTOG00000012446
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B, delta [Source:HGNC Symbol;Acc:23732]

Sequence

>retro_itri_381
ACTGAACGGGATAAAAGAGCAGAAGGTTATAACTTGAAAGATGAAGATGGACGACTCCGAGACCCATTTAGAATCACAGC
ACTGCGGGTTCCAATATTGAAGCCCATGGACCTCATGGTAGAAGCAAGCCCACGACCAATTTTTGCAAATGCTGATACAT
GTCATATAAATTACATTTCAGTAAATAGTGATCATGAAACGTATCTTTCTGCAGATGACCTGAGAATTAACCTGTGGCAT
TTAGAAATCACAGATAGAAGTTTTAATATCGTGGACATCAAACCTGCCACCATGGAGGAGCTGACCGAGGTGATCACCGC
TGCCGAGTTCCACCCACACCAGTGCAACGTGTTCATGTACAGCAGCAGCAAAGGGACCATCCGGCTGTGTGACATGCGCT
CCTCCGCCCTGTGCGACCGGCACTCTCTAAGTTTTTTGAAGAGCCTGAAGATCTCAGTTAGTAGGTCCTTCTTCTCAGAA
ATAATCTCATCCATATCCGACGTCAAATTCAGCCATAGTGGTCGGTACATGATGACCCGAGACTACCTGTCAGTGAAGGT
GTGGGACCTCAACATGGAGAGCAGGCCAGTGGAGACCCACCAGGTACATGAGTACCTGCGGAGCAAGCTCTGCTCCTTCT
ACGAGAACGACTGCATCTTCGACAAGTTTGAGTGCTGCTGGAACGGTTCCGACAGTGCTGTCGTGACGGGCTCCTACAAC
AACTTCTTCAGGATGTTCGACAGAAGCATGCGCAGGGATGTCACCCTGGAAGCCTCAAAAGAGAGCAGCAAACCCTGAGC
CAGCTTAAAGCCCCGGAAAGTTTGTGCAGGTGGGAAGAGGAAGAAGGATGAGATCAGTGTGGACAGCCTGGACTTCAATA
AGAACATCCTCCACACAGCCTGGCACCCCGTGGACAACATCATTGCCGTGGCCGCCACCAACAACCTGTACATATTCAAG
GACAAAGCCAAC

Alignment

ORF - retro_itri_381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 76.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SERDKRAEGYNLKDEDGRLRDPFRITALRVPILKPMDLMVEASPRRIFANAHTYHINSISVNSDHETYLS
          .ERDKRAEGYNLKDEDGRLRDPFRITALRVPILKPMDLMVEASPR.IFANA.T.HIN.ISVNSDHETYLS
Retrocopy TERDKRAEGYNLKDEDGRLRDPFRITALRVPILKPMDLMVEASPRPIFANADTCHINYISVNSDHETYLS

Parental  ADDLRINLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHPHQCNVFVYSSSKGTIRLCDMRSSALCDR
          ADDLRINLWHLEITDRSFNIVDIKPA.MEELTEVITAAEFHPHQCNVF.YSSSKGTIRLCDMRSSALCDR
Retrocopy ADDLRINLWHLEITDRSFNIVDIKPATMEELTEVITAAEFHPHQCNVFMYSSSKGTIRLCDMRSSALCDR

Parental  HS-KFFEEPEDPSSRSFFSEIISSISDVKFSHSGRYMMTRDYLSVKVWDLNMESRPVETHQVHEYLRSKL
          HS..F........SRSFFSEIISSISDVKFSHSGRYMMTRDYLSVKVWDLNMESRPVETHQVHEYLRSKL
Retrocopy HSLSFLKSLKISVSRSFFSEIISSISDVKFSHSGRYMMTRDYLSVKVWDLNMESRPVETHQVHEYLRSKL

Parental  CSLYENDCIFDKFECCWNGSDSSAVMTGSYNNFFRMFDRSTRRDVTLEASRESSKPRASLKPRKVCAGGK
          CS.YENDCIFDKFECCWNGSD.SAV.TGSYNNFFRMFDRS.RRDVTLEAS.ESSKP.ASLKPRKVCAGGK
Retrocopy CSFYENDCIFDKFECCWNGSD-SAVVTGSYNNFFRMFDRSMRRDVTLEASKESSKP*ASLKPRKVCAGGK

Parental  RKKDEISVDSLDFNKKILHTAWHPVDNIIAVAATNNLYIFQDKAN
          RKKDEISVDSLDFNK.ILHTAWHPVDNIIAVAATNNLYIF.DKAN
Retrocopy RKKDEISVDSLDFNKNILHTAWHPVDNIIAVAATNNLYIFKDKAN

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_381 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_381 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000016940	1 retrocopy	retro_rnor_1393,
Ictidomys tridecemlineatus	ENSSTOG00000012446	1 retrocopy	retro_itri_381 ,