RetrogeneDB ID: retro_itri_1553

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393537.1:2261723..2262254(-)
• 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_1553
CTGAGGTTTCTTGCAAACCATACTAATATTTTACTGGCATCTTTAATCTTCTATACAATATTTTTATGCCCATGGGATCT
AATTTCCTAGGGCTATTCATTCTTAATATGCTCGACTTCTGGCTGTGGGAATGAAGGAGTGATCAGAACTTGGAAATAGT
AGGTGGAGTCACACATGCTAATAGCTATTACAAAAATGGCTGGCTAGTCATGATAGCTATTGGATGGACCCAAGGTGCAG
GTGGTATCATTATCATGAATTTTGAATAGTTGGTAAAAGGAGATTGGAACCCAGAAGAAGAGGAGTGGCTGAAGATGTCC
TGTCTTTCCAAGGTAATCTTGCTGGGGTCCCTTATCTTCTTCACATTTCAGCACACCAAGTATCTGATCATATCAAAGCA
TAATCTTATTCCTTTATACCATCTTTCTTGTGGCCACAAAGATAACCATGATGGTTACAGAGACTTCTGTGACTCTTGCT
CCTTTTGAGCATATATTGAGTTGGCTGCTCTTTGGCTGGCAGCAACAGTTC

Alignment

ORF - retro_itri_1553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.63 %
• Parental protein coverage: 61.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LRFFANHTNVLLASSIWYIIFFCPWDLISQGYSFLP-VQLLAAGMKE-VTRTWK-IIGGITHANSYYKNG
          LRF.ANHTN.LLAS.I.Y.IF.CPWDLIS.GYSFL....LLA.GMKE.V.RTWK.I.GG.THANSYYKNG
Retrocopy LRFLANHTNILLASLIFYTIFLCPWDLIS*GYSFLI>ARLLAVGMKE<VIRTWK<IVGGVTHANSYYKNG

Parental  WLVMIAIGWAQGAGGIIITNFEQLLKGDWKPEGNEWLKMSYPSKVTLLGSLI-FTFQHTKHLTISKHNLM
          WLVMIAIGW.QGAGGIII.NFE.L.KGDW.PE..EWLKMS..SKV.LLGSLI.FTFQHTK.L.ISKHNL.
Retrocopy WLVMIAIGWTQGAGGIIIMNFE*LVKGDWNPEEEEWLKMSCLSKVILLGSLIFFTFQHTKYLIISKHNLI

Parental  FLYTI-FL-VTTKITMMITETSSVTLAPFEDILSRMLFGWQHQF
          .LY...FL.V.TKITMM.TET.SVTLAPFE.ILS..LFGWQ.QF
Retrocopy PLYHL<FL<VATKITMMVTET-SVTLAPFEHILSWLLFGWQQQF

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_1553 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1553 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,