RetrogeneDB ID: retro_itri_1823

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393911.1:111051..111646(-)
• 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_1823
GCTATGCTCCACTGCTTTGGTGGAGGATTTTTATCGTGTGTACTGCTTACAGAGCTTCCTCTGAGGTTTCTTGCAAACCA
CACTAATATTTTACTGGCATCTTCAATCATCTATACAATATTTTTTTTGCCCATGGGATCTAATTTCCTAGGGCTATTCA
TTCTTAATATGCTCAACTTCTGGCTGTGGGAATGAAGGAGTGATCAGAACTTGGAAAATAGTAGGTGGAGTCACACATGC
TAACAGCTATTACAAAAATGGCTGGCTAGTCATGATAGCTATTAGATGGGCCCAAGGTGCAGGTGGTATCATTATCATGA
ATTTTGAATAGTTGGTAAAAGGAGATTGGAACCCAGAAGAAGTGGAGTGGCTGAAGATGTCCTGTCTTTCCAAGGTAATC
TTGCTGGAGTCCCTTATCTTCTTCACATTTCAGCACACCAAATATCTGACCATATCAAAGCATAACCTTATGTTCCTTTA
TACCATCTTTCTTGTGGCCACAAAGATAACCATGATGGTTACAGAGACTTCTGTGACTCTTGCTCCTTTTGAGCATATAT
TGAGTAGGCTGCTCTTTGGCTGGCAGCAACAGTTC

Alignment

ORF - retro_itri_1823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.2 %
• Parental protein coverage: 68.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AMLHCFGGGILSCILLAEPPLRFFANHTNVLLASSIWYIIFFCP-WDLISQGYSFLP-VQLLAAGMKE-V
          AMLHCFGGG.LSC.LL.E.PLRF.ANHTN.LLASSI.Y.I...P.WDLIS.GYSFL...QLLA.GMKE.V
Retrocopy AMLHCFGGGFLSCVLLTELPLRFLANHTNILLASSIIYTIXXXP>WDLIS*GYSFLI>AQLLAVGMKE<V

Parental  TRTWKIIGGITHANSYYKNGWLVMIAIGWAQGAGGIIITNFEQLLKGDWKPEGNEWLKMSYPSKVTLLGS
          .RTWKI.GG.THANSYYKNGWLVMIAI.WAQGAGGIII.NFE.L.KGDW.PE..EWLKMS..SKV.LL.S
Retrocopy IRTWKIVGGVTHANSYYKNGWLVMIAIRWAQGAGGIIIMNFE*LVKGDWNPEEVEWLKMSCLSKVILLES

Parental  LI-FTFQHTKHLTISKHNLMFLYTIFLVTTKITMMITETSSVTLAPFEDILSRMLFGWQHQF
          LI.FTFQHTK.LTISKHNLMFLYTIFLV.TKITMM.TET.SVTLAPFE.ILSR.LFGWQ.QF
Retrocopy LIFFTFQHTKYLTISKHNLMFLYTIFLVATKITMMVTET-SVTLAPFEHILSRLLFGWQQQF

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_1823 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1823 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,