RetrogeneDB ID: retro_itri_1708

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393647.1:888527..889257(-)
• 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_1708
ATGGACTCTCCATGGGAGGAGCTGGCACTGGCCTTCTCTTGCATGTCCATGTTCCCCTTTTTGGACATCACCCACATCTG
GTGTCTGTGATGGCACTGAAGCATCAGCTGGTAGGAGTGGAAGGGGCATGGAAGAATCCTGTTTCAAGCTGGTCTACTGC
TATACTCCCTGATTTAGTGGAGGAATTTTAACATGTGTACTGCTTGAAGAGCCTCCACTGAGGTTTCTTCCAAACCACAT
TAATATTTTACTGGCATCTTCAATCTGGTATATTACATATATTTTTGCCCATGGGACCTAAATTCCCAGGACTATTCATT
CTTATCTGCTCAACTTCTGGCTGTGGGAATGAAGGAGTGATCAGAACTTGGAAAATAGAAGGTGGAGTCACACATGCTAA
TAGCTATTACAAAAATGGCTGGCCAGTCATGATAGCTATTGGATGGGCCCAAGGTGCAGGTGGTATCACTATCATGAATT
TTGAATAGTTGGTAAAAGGAGATTGGAAACCAGAGATGATGAATGATGAAAGATGTCCTGTCCTTCCAAGGTAACCTTGC
TGGGGTCCCTTCACATTTCAGCACACCAAGCATCTGACCACACCAAGCATAATTTTATGTTCCTTTATACCATCTTTCTT
GTGGCCAAAAAGATAACCATCATAGTTACACAGTTTTCTTCTATGACTCTTAGTCCTTTTGAATATGTATTGAGTTGGCT
GCTCTTTGGC

Alignment

ORF - retro_itri_1708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.98 %
• Parental protein coverage: 84.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MDSSWEDLTLAFSRTSMFPFFDIAH-YLVSVMALKHRPGAVEGAWKNPFSSWFTAMLHC-FGGGILSCIL
          MDS.WE.L.LAFS..SMFPF.DI.H..LVSVMALKH....VEGAWKNP.SSW.TA.L...F.GGIL.C.L
Retrocopy MDSPWEELALAFSCMSMFPFLDITH<HLVSVMALKHQLVGVEGAWKNPVSSWSTAILPD<FSGGILTCVL

Parental  LAEPPLRFFANHTNV-LLAS-SIWYIIFFCPWDLISQGYSFLPVQLLAAGMKE-VTRTWKIIGGITHANS
          L.EPPLRF..NH.N..L..S....Y.I.FCPWDL.SQ.YSFL..QLLA.GMKE.V.RTWKI.GG.THANS
Retrocopy LEEPPLRFLPNHINILLASS<NLVYYIYFCPWDLNSQDYSFLSAQLLAVGMKE<VIRTWKIEGGVTHANS

Parental  YYKNGWLVMIAIGWAQGAGGIIITNFEQLLKGDWKPE-GNEWLKMSYPSKVTLLGSL-IFTFQHTKHLTI
          YYKNGW.VMIAIGWAQGAGGI.I.NFE.L.KGDWKPE...E..KMS.PSKVTLLGSL.I...Q...H...
Retrocopy YYKNGWPVMIAIGWAQGAGGITIMNFE*LVKGDWKPE<DDE**KMSCPSKVTLLGSLHISAHQASDH---

Parental  SKHNLMFLYTIFLVTTKITMMITETSSVTLAPFEDILSRMLFG
          .KHN.MFLYTIFLV..KIT...T..SS.TL.PFE..LS..LFG
Retrocopy TKHNFMFLYTIFLVAKKITIIVTQFSSMTLSPFEYVLSWLLFG

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_1708 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1708 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,