RetrogeneDB ID: retro_itri_678

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393310.1:662313..662629(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50B
• Ensembl ID: ENSSTOG00000023740
• Aliases: None
• Description: transmembrane protein 50B [Source:HGNC Symbol;Acc:1280]

Sequence

>retro_itri_678
GCTTCCCACCCATGTGGTGTGTTTCCACATTGGCTTTCCTTACTTGAGCATGAAGGATAAGTGCTGCACTGAACGTCCAG
GTGAGCAGTGACAGCCAGGGGAGCAGCTGGTTAAGAAGAACAAGTGCCTGAGTTTGCCTCCTCCTTGGTTTCACGTTGAT
GTCTGGGTCACTTATTGCTTCCAGTGGATTCTTTTTGGTGCATGTTACTCAAAATACTAATCTTTATCCAGGACTAGCTG
TGTTGTTTTTCAAAATGCTCTTATATTTTTTAGCACTTTGATCTTCAAATTTGGAAGAACTGAAGAGCTCTGAACC

Alignment

ORF - retro_itri_678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 64.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AFHTCGVF-STLAFFM----INAVSNAQVRGDSYESGCLGRTGARVWLFIGFMLMFGSLIAS-MWILFGA
          A.H.CGVF.STLAF......I.A..N.QV..DS..S..L.RT.A.V.L..GF.LM.GSLIAS..WILFGA
Retrocopy ASHPCGVF<STLAFLT*A*RISAALNVQVSSDSQGSSWLRRTSA*VCLLLGFTLMSGSLIAS<QWILFGA

Parental  YVTQNTDVYPGLAVFFQNALIFFSTLIYKFGRTEELWT
          .............V.FQNALIFFSTLI.KFGRTEEL.T
Retrocopy CYSKY*SLSRTSCVVFQNALIFFSTLIFKFGRTEEL*T

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_678 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_678 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003928	1 retrocopy	retro_chof_422,
Myotis lucifugus	ENSMLUG00000012388	1 retrocopy	retro_mluc_970,
Nomascus leucogenys	ENSNLEG00000003887	1 retrocopy	retro_nleu_2077,
Pan troglodytes	ENSPTRG00000013869	1 retrocopy	retro_ptro_1379,
Ictidomys tridecemlineatus	ENSSTOG00000022246	2 retrocopies	retro_itri_1228, retro_itri_1329,
Ictidomys tridecemlineatus	ENSSTOG00000023740	1 retrocopy	retro_itri_678 ,