RetrogeneDB ID: retro_itri_1329

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393442.1:4257104..4257555(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50A
• Ensembl ID: ENSSTOG00000022246
• Aliases: None
• Description: transmembrane protein 50A [Source:HGNC Symbol;Acc:30590]

Sequence

>retro_itri_1329
GGATTTCTGGAAGGTTTGAGATGCTCAGAATGCATTGATTTGGGGTGGTGGATAATGAACTACTATTTCCATTGCTGCTG
ATGTTGTTTTTCATAGGCCAGTTGATTATCATAGATGCACCTGTTATTTTTCCCACTATGGAAGAGTTCAATCACTCATA
CTGTGCCTGCTGTGTGATAGCAGCCACAGCTTCCTAATGATTAGTGGACAAGTCAAGGATGGCAGTTACAGTGAACTCTG
TTCTGGATCAAACAGTACTCACATTTGGCTCTTCATAGGTTTCGTGTTCTCCTTTCGATCTCTGATGGCATCTATGTGGA
TTCTTTTTGGAGGTTATGTTGCTAAAGAAAGATCAATGGTACATCCTGGAATTGCTGTGTTTTTCCAGAATCCTTTTATC
TTTTTTGGAGGACTGGTTCTTAAGTTGGGTCACACAGAAGACTTATGGCAG

Alignment

ORF - retro_itri_1329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.33 %
• Parental protein coverage: 98.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFLEGMRCSECID-WGEKRNTIASVAAGVLFFTGWWIIIDAAVMYPTMEEFNHSYHACGVIATIA-FLMI
          GFLEG.RCSECID..G...N.........LFF.G..IIIDA.V..PTMEEFNHSY.AC.VIA..A.FLMI
Retrocopy GFLEGLRCSECID<FGVVDNELLFPLLLMLFFIGQLIIIDAPVIFPTMEEFNHSYCACCVIAATA<FLMI

Parental  NAVSNGQVRGDSYSEGCLGQTGARIWLFLGFMLAFGSLITSMWILFGGYVAKEKPIVYPGIAVFFQNAFI
          .....GQV...SYSE.C.G.....IWLF.GF...F.SL..SMWILFGGYVAKE...V.PGIAVFFQN.FI
Retrocopy S----GQVKDGSYSELCSGSNSTHIWLFIGFVFSFRSLMASMWILFGGYVAKERSMVHPGIAVFFQNPFI

Parental  FFGGLVFKFGRTEDLWQ
          FFGGLV.K.G.TEDLWQ
Retrocopy FFGGLVLKLGHTEDLWQ

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_1329 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1329 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018575	1 retrocopy	retro_cjac_1677,
Cavia porcellus	ENSCPOG00000012615	1 retrocopy	retro_cpor_707,
Echinops telfairi	ENSETEG00000007483	1 retrocopy	retro_etel_2061,
Macropus eugenii	ENSMEUG00000002060	1 retrocopy	retro_meug_1270,
Macaca mulatta	ENSMMUG00000032217	1 retrocopy	retro_mmul_1408,
Ochotona princeps	ENSOPRG00000001182	2 retrocopies	retro_opri_546, retro_opri_62,
Pongo abelii	ENSPPYG00000001711	1 retrocopy	retro_pabe_1679,
Ictidomys tridecemlineatus	ENSSTOG00000022246	2 retrocopies	retro_itri_1228, retro_itri_1329 ,
Ictidomys tridecemlineatus	ENSSTOG00000023740	1 retrocopy	retro_itri_678,