RetrogeneDB ID: retro_itri_1159

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393390.1:204926..205281(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSPH
• Ensembl ID: ENSSTOG00000026898
• Aliases: None
• Description: phosphoserine phosphatase [Source:HGNC Symbol;Acc:9577]

Sequence

>retro_itri_1159
AGGTAGATGGTAAATTGCCTACAAATATGAAACGTTCAGATTTTCCCAATATCTGATGGCTTTAGAAGTATTGTAGAGCA
TGTTACTTCAAAGCTCAATATGCCAGCAACCAATATATCTGCCAATAGGCTGAAATTCTACTTTAATAGGACTACACAGG
TTTTGATGAGACACAGCCAACAGTCCAATCTGGTGGGAAAGGAAAAATACTAAATTTTTAAAAGAAAATTTCTACTTCAA
GAAAATAATCATGATTAGAGATGTAGCTACAAATATGGAAGCCTATCCTCCTGCTGATGTTTTCATTGGGTTTAGAGGAA
ATGTGATTGGGCAACAAGTAAAGGACACTGCCAAA

Alignment

ORF - retro_itri_1159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.9 %
• Parental protein coverage: 52.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RELVSRLQERNVQVFLISGGFRSIVEHVAAKLNIPAANVFANRLKFYFNG-EYAGFDETQPTADSGGKGK
          R..V..LQ..NVQ.F.IS.GFRSIVEHV..KLN.PA.N..ANRLKFYFN...Y.GFDETQPT..SGGKGK
Retrocopy R*MVNCLQI*NVQIFPISDGFRSIVEHVTSKLNMPATNISANRLKFYFNR<DYTGFDETQPTVQSGGKGK

Parental  VI-KFLKEKFHFKKIIMIGDGATDMEACPPADVFIGFGGNVIRQQVKDNAR
          ...KFLKE.F.FKKIIMI.D.AT.MEA.PPADVFIGF.GNVI.QQVKD.A.
Retrocopy IL<KFLKENFYFKKIIMIRDVATNMEAYPPADVFIGFRGNVIGQQVKDTAK

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_1159 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1159 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016118	1 retrocopy	retro_amel_607,
Felis catus	ENSFCAG00000021883	1 retrocopy	retro_fcat_183,
Ictidomys tridecemlineatus	ENSSTOG00000026898	1 retrocopy	retro_itri_1159 ,