RetrogeneDB ID: retro_itri_188

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:6378278..6378529(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSSTOG00000012662
• Aliases: None
• Description: LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17162]

Sequence

>retro_itri_188
AACCCATCAAAGATGCTGCTGCTAGAACTTGCGGACAGTGCATAGGATCAAAAATTCACATTGTGATGAAGAGTGATAAG
GAAATTGTTGGAACACATCTAGGATTTGATGATGTTGTCAATATGGTGCTGGAAGATGTCACAGAGTTTAAAATCACACC
AGAAGGTAGAAGGATTACTAAATTAAATCATATTTTGCTAAGTGGAAATAAAATAATAATGCTGGTTTCTAGAGGAAAAG
GACCTGAAGTA

Alignment

ORF - retro_itri_188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.82 %
• Parental protein coverage: 92.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPSQLLPLELVD-KCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRITKLDQILLNG
          NPS..L.LEL.D..CIGS.IHIVMKSDKEIVGT.LGFDD.VNMVLEDVTEF.ITPEGRRITKL..ILL.G
Retrocopy NPSKMLLLELAD<QCIGSKIHIVMKSDKEIVGTHLGFDDVVNMVLEDVTEFKITPEGRRITKLNHILLSG

Parental  NNITMLVPGGEGPEV
          N.I.MLV..G.GPEV
Retrocopy NKIIMLVSRGKGPEV

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_188 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_188 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 8 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005335	1 retrocopy	retro_chof_1042,
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Dasypus novemcinctus	ENSDNOG00000008121	1 retrocopy	retro_dnov_1836,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Ictidomys tridecemlineatus	ENSSTOG00000012662	4 retrocopies	retro_itri_1199, retro_itri_188 , retro_itri_222, retro_itri_415,
Tarsius syrichta	ENSTSYG00000006449	9 retrocopies	retro_tsyr_1022, retro_tsyr_1080, retro_tsyr_1579, retro_tsyr_181, retro_tsyr_1837, retro_tsyr_1863, retro_tsyr_1963, retro_tsyr_577, retro_tsyr_96,