RetrogeneDB ID: retro_itri_1826

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393920.1:121039..121569(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM38B
• Ensembl ID: ENSSTOG00000003014
• Aliases: None
• Description: transmembrane protein 38B [Source:HGNC Symbol;Acc:25535]

Sequence

>retro_itri_1826
ATGGACTCTCCATGGGAAAAGCTGGCATTGGCCTTCTCCTGCACGTCCATGTTCCCCTTTTTTTTGACATCACCCACATC
TGTTGTCTGTGATGGCCTTGAAGCATCAGCTGGTAGGAGTGGAAGGAGCATGGAAGAATCCTGTTTCAAGCTGGTCTACT
GCTTTGATCCCTGATTTGGTGGAGAAATTTTAACATGTGTACTGCTTGAAGAGCCTCCACTGAGGTTTCTTGCAAACCCC
ATTAATATTTTACTGGCATCTTCAATCTGGTATATTACATATATTTTTGCCCATGGGACCTAAATTCCCAGGACTATTCA
TTCTTATCCGCTCAACTTCTGGCTGTGGGAATGAAGGAGTGATAAGAATTTGGAAATTAGAAGGTGGAATCACACATGCT
AATAGCTATTACAAAAATGGCTGGCCAGTCATGATAGCTATTGGATGGGCCCAAGGTGCAGCTGGTATCACTATCATGAA
TTTTGAACAGTTGGTAAAGGAGATTGGAAACCAGAGATGATGAATGGCTT

Alignment

ORF - retro_itri_1826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• Parental protein coverage: 60.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MDSSWEDLTLAFSRTSMFPFFDIA-HYLVSVMALKHRPGAVEGAWKNPFSSWFTAMLHC-FGGGILSCIL
          MDS.WE.L.LAFS.TSMFP........L.SVMALKH....VEGAWKNP.SSW.TA.....FGG.IL.C.L
Retrocopy MDSPWEKLALAFSCTSMFPXXXTS>PHLLSVMALKHQLVGVEGAWKNPVSSWSTALIPD<FGGEILTCVL

Parental  LAEPPLRFFANHTNVLLASSIWYIIF-FCP-WDLISQGYSFLPVQLLAAGMKE-VTRTWKIIGGITHANS
          L.EPPLRF.AN..N.LLASSIWYI...F.P.WDL.SQ.YSFL..QLLA.GMKE.V.R.WK..GGITHANS
Retrocopy LEEPPLRFLANPINILLASSIWYITY>FLP>WDLNSQDYSFLSAQLLAVGMKE<VIRIWKLEGGITHANS

Parental  YYKNGWLVMIAIGWAQGAGGIIITNFEQLL-KGDWKPE-GNEWL
          YYKNGW.VMIAIGWAQGA.GI.I.NFEQL..KGDWKPE...EWL
Retrocopy YYKNGWPVMIAIGWAQGAAGITIMNFEQLV<KGDWKPE<DDEWL

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_1826 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1826 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002467	1 retrocopy	retro_chof_1110,
Ictidomys tridecemlineatus	ENSSTOG00000003014	7 retrocopies	retro_itri_1553, retro_itri_1708, retro_itri_1789, retro_itri_1823, retro_itri_1824, retro_itri_1826 , retro_itri_1845,