RetrogeneDB ID: retro_itri_212

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:40749931..40750186(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOHB
• Ensembl ID: ENSSTOG00000000835
• Aliases: None
• Description: mago-nashi homolog B (Drosophila) [Source:HGNC Symbol;Acc:25504]

Sequence

>retro_itri_212
ATGGCTATGGCTAGTGATTTCTATCTATGCTACTATGTAGAGCACAAGGGCAAGTTTGGACATGAGTTTCTAGAGTTCGA
GTTTCAGCCAGATGGAAAACCTAGATATGCAAACAACAGCAATTACAAAAATGATGTCATGATCAGGAAAGAGGCATATG
TACATAGGAGTGTAATGGAAGAACTGAAGGGAATTATTAATGACAGTGATATCACAAAAGAAGATGATTCCCTGTGGTCT
CCTCCTGTCAGGGTG

Alignment

ORF - retro_itri_212 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.88 %
• Parental protein coverage: 59.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSMASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSE
          M.MASDFYL.YYV.HKGKFGHEFLEFEF.PDGK.RYANNSNYKNDVMIRKEAYVH.SVMEELK.II.DS.
Retrocopy MAMASDFYLCYYVEHKGKFGHEFLEFEFQPDGKPRYANNSNYKNDVMIRKEAYVHRSVMEELKGIINDSD

Parental  ITKEDDALWPPPDRV
          ITKEDD.LW.PP.RV
Retrocopy ITKEDDSLWSPPVRV

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_212 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_212 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 15 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004382	1 retrocopy	retro_chof_1730,
Callithrix jacchus	ENSCJAG00000021662	7 retrocopies	retro_cjac_1336, retro_cjac_1840, retro_cjac_1858, retro_cjac_2354, retro_cjac_3234, retro_cjac_3250, retro_cjac_546,
Dasypus novemcinctus	ENSDNOG00000005997	4 retrocopies	retro_dnov_140, retro_dnov_347, retro_dnov_423, retro_dnov_891,
Echinops telfairi	ENSETEG00000016591	3 retrocopies	retro_etel_1022, retro_etel_1566, retro_etel_2147,
Homo sapiens	ENSG00000111196	1 retrocopy	retro_hsap_1360,
Macropus eugenii	ENSMEUG00000001782	1 retrocopy	retro_meug_324,
Macaca mulatta	ENSMMUG00000005082	1 retrocopy	retro_mmul_1246,
Monodelphis domestica	ENSMODG00000000462	1 retrocopy	retro_mdom_424,
Nomascus leucogenys	ENSNLEG00000003355	1 retrocopy	retro_nleu_1395,
Ochotona princeps	ENSOPRG00000000548	2 retrocopies	retro_opri_1171, retro_opri_308,
Pan troglodytes	ENSPTRG00000004679	2 retrocopies	retro_ptro_1179, retro_ptro_932,
Ictidomys tridecemlineatus	ENSSTOG00000000835	1 retrocopy	retro_itri_212 ,
Ictidomys tridecemlineatus	ENSSTOG00000001253	3 retrocopies	retro_itri_373, retro_itri_379, retro_itri_932,
Tupaia belangeri	ENSTBEG00000014820	7 retrocopies	retro_tbel_1250, retro_tbel_1393, retro_tbel_210, retro_tbel_2259, retro_tbel_2723, retro_tbel_2878, retro_tbel_451,
Tarsius syrichta	ENSTSYG00000010452	7 retrocopies	retro_tsyr_1730, retro_tsyr_1748, retro_tsyr_383, retro_tsyr_658, retro_tsyr_81, retro_tsyr_908, retro_tsyr_966,