RetrogeneDB ID: retro_itri_1789

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393785.1:180062..180714(-)
• 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_1789
TTTTTGGTGTCTGTGATGGCACTGAAGCATCAGCTGGTAGGAGTGGAAAGAGCATGGAAGAATCCTGTTTCAAGCTTGTC
ACTGCTATGCTCCCTGATTTGGTGGAGGAATTTTAACATGTGTACTCCTTGAAGAGGCTCCACTAAGGTTTCTTCCAAAC
CACATTAATATTTTACTGGCATCTTCAATCTGGTATATATTTTTTTGCCCATGGGACCTAATTTCCTAGGGCTATTCATT
CTTAACCTGCTCAACTTCTGGCAGTGTGGATGAAGGAAATGACCAGAACTTGGAAAATAGAAGGTGGAATCACACATGCT
AATAGCTATTACAAAAATGGCTGGCCAGTCATGATAGCTATTGGATGGGCCCAACGTGCAGGGGGCATCATTATCATGAA
TTTTGAATAGTTGGTAAAGGAGATTGGAAACCAGAGATGATGAATGGCTTAAGATGTCCTATCCTTTCAAGGTAACCTTG
CTGGGGTCCCTTCACATTTCAGCACACCCAGCATCTCACCACATCAAAGCATAATCTTATGTTCCTTTATACCACCTTTC
TTGTGGCCAAAAAGATAACCATCATGGTTACACAGACTTCTTCTATGACTCTTAGTCCTTTTGAGGATATATTGAGTTGG
CTGCTCTTTGGC

Alignment

ORF - retro_itri_1789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.56 %
• Parental protein coverage: 75.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YLVSVMALKHRPGAVEGAWKNPFSSW-FTAMLHC-FGGGILSCILLAEPPLRFFANHTNVLLASSIWYII
          .LVSVMALKH....VE.AWKNP.SS...TAML...FGGGIL.C.LL.E.PLRF..NH.N.LLASSIWYI.
Retrocopy FLVSVMALKHQLVGVERAWKNPVSSL<VTAMLPD<FGGGILTCVLLEEAPLRFLPNHINILLASSIWYI-

Parental  FFCPWDLISQGYSFL-PVQLLAAGMKEVTRTWKIIGGITHANSYYKNGWLVMIAIGWAQGAGGIIITNFE
          FFCPWDLIS.GYSFL.P.QLLA..MKE.TRTWKI.GGITHANSYYKNGW.VMIAIGWAQ.AGGIII.NFE
Retrocopy FFCPWDLIS*GYSFL>PAQLLAVWMKEMTRTWKIEGGITHANSYYKNGWPVMIAIGWAQRAGGIIIMNFE

Parental  QLLK-GDWKPEGNEWLKMSYPSKVTLLGSLIFTFQHTKHLTISKHNLMFLYTIFLVTTKITMMITETSSV
          .L.K.GDWKPE....L.....S.....G...FTFQHT.HLT.SKHNLMFLYT.FLV..KIT.M.T.TSS.
Retrocopy *LVK<GDWKPEMMNGLRCPILSR*PCWGP--FTFQHTQHLTTSKHNLMFLYTTFLVAKKITIMVTQTSSM

Parental  TLAPFEDILSRMLFG
          TL.PFEDILS..LFG
Retrocopy TLSPFEDILSWLLFG

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_1789 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1789 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,