RetrogeneDB ID: retro_itri_1169

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393392.1:4386546..4387102(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSSTOG00000000660
• Aliases: None
• Description: chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]

Sequence

>retro_itri_1169
TCTGAACAGGCAGCATTAACACTTTAGCAGGAGAAGTTAAAGCAGCACTTGGGTAAGAGTAATATCCAAGCGAGGTCAGG
CCGACTCATAGGGGTCCTGGCCATGGGAGCAATTGGAGGATAAGTTATGTTCATAATCCAGAGAGACTTATCCAGAGGAA
GACAACGTGAGGGATGTACCACCAGAACCCTACTTAGAGACAGGATATCGCTCTGAGGTCAAAACCTGCTCCTAGGTGAA
CTAGCCATAGCTCCCCAAATGGGCTTAAGAAGAGGTGATGTTCAAAGTCACAGAGGCTCTGGGAAAGGGGGCCTGGAGCG
TGGAGCTATGGTAGTGGCTACATTAGTGGTAGAAGTCGGGGCAAGATAGGACAGTGAAAGGGGGTTTTGGAGGCCGAAGA
CAAGACAATGGACCAGGGAAAGGTGCCCTCACTCCCCTATATTGACCAAGGAGCCACTGGACAACCAGTTGGATGCACAC
ATGTTTAAAACTGAAGCCTATCTGGATGCAGAGTTGGATGCTTACATTGGCACAGACAAATCCAGAAACCAACGAT

Alignment

ORF - retro_itri_1169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.79 %
• Parental protein coverage: 74.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVQAALKLKQKSLKQRLGKSNIQARLGRPIGALARGAIGGRGLPIIQRGLSRGGLRGGRATRTLLRGGMS
          S.QAAL.L.Q..LKQ.LGKSNIQAR.GR.IG.LA.GAIGG....IIQR.LSRG..R.G..TRTLLR...S
Retrocopy SEQAALTL*QEKLKQHLGKSNIQARSGRLIGVLAMGAIGG*VMFIIQRDLSRGRQREGCTTRTLLRDRIS

Parental  LRGQNLLRGGRAVAPRMGLRRGGVRGRGGPGRGGLGRGAM-GRGGIGGRGRGMIGR-GRGGFGGRGRGRG
          L.GQNLL.G..A.AP.MGLRRG.V....G.G.GGL.RGAM.G.G.I.GR.RG.IG....GGFGGR....G
Retrocopy L*GQNLLLGELAIAPQMGLRRGDVQSHRGSGKGGLERGAM<GSGYISGRSRGKIGQ<VKGGFGGRRQDNG

Parental  RGRGALT-RPVLTKEQLDNQLDAYMSKTKGHLDAELDAY-MAQTDPETND
          .G.GALT..P.LTKE.LDNQLDA.M.KT...LDAELDAY..AQT.PETND
Retrocopy PGKGALT<SPILTKEPLDNQLDAHMFKTEAYLDAELDAY>LAQTNPETND

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_1169 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1169 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Callithrix jacchus	ENSCJAG00000010383	3 retrocopies	retro_cjac_2059, retro_cjac_423, retro_cjac_431,
Felis catus	ENSFCAG00000002740	1 retrocopy	retro_fcat_1925,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Mus musculus	ENSMUSG00000001017	2 retrocopies	retro_mmus_1693, retro_mmus_1852,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Ictidomys tridecemlineatus	ENSSTOG00000000660	1 retrocopy	retro_itri_1169 ,
Tupaia belangeri	ENSTBEG00000012442	1 retrocopy	retro_tbel_293,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,