RetrogeneDB ID: retro_itri_1597

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393564.1:1641646..1641874(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1B
• Ensembl ID: ENSSTOG00000012168
• Aliases: None
• Description: eukaryotic translation initiation factor 1B [Source:HGNC Symbol;Acc:30792]

Sequence

>retro_itri_1597
CAAGATGGCAGGAAGACACTGACTACAGTTCAGGGCATTGCAGATGATTATGACAAAAAGAAACTTGTGAAAGCTTTCAA
AAAGAAATTTGCCTGTAATGGTTCTGTGATTGAACATCCTGAATACGGGGAGGTTATTCAACTTCAAGGTGACCAAAGAA
AAAACATTTGCCAGTTTCTCTTGGAGGTTGGCATTGTCAAGGAGGAGCAGCTTAAGGTTCACAGATTC

Alignment

ORF - retro_itri_1597 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 67.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RNGRKTLTTVQGIADDYDKKKLVKAFKKKFACNGTVIEHPEYGEVIQLQGDQRKNICQFLLEVGIVKEEQ
          ..GRKTLTTVQGIADDYDKKKLVKAFKKKFACNG.VIEHPEYGEVIQLQGDQRKNICQFLLEVGIVKEEQ
Retrocopy QDGRKTLTTVQGIADDYDKKKLVKAFKKKFACNGSVIEHPEYGEVIQLQGDQRKNICQFLLEVGIVKEEQ

Parental  LKVHGF
          LKVH.F
Retrocopy LKVHRF

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_1597 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1597 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 11 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013689	4 retrocopies	retro_dord_179, retro_dord_307, retro_dord_626, retro_dord_669,
Echinops telfairi	ENSETEG00000017295	5 retrocopies	retro_etel_1228, retro_etel_1480, retro_etel_1793, retro_etel_31, retro_etel_4,
Microcebus murinus	ENSMICG00000013223	5 retrocopies	retro_mmur_254, retro_mmur_445, retro_mmur_535, retro_mmur_654, retro_mmur_706,
Macaca mulatta	ENSMMUG00000017704	1 retrocopy	retro_mmul_154,
Monodelphis domestica	ENSMODG00000011056	2 retrocopies	retro_mdom_1113, retro_mdom_1382,
Mus musculus	ENSMUSG00000006941	1 retrocopy	retro_mmus_587,
Otolemur garnettii	ENSOGAG00000025224	1 retrocopy	retro_ogar_1943,
Ictidomys tridecemlineatus	ENSSTOG00000002719	15 retrocopies	retro_itri_1082, retro_itri_1184, retro_itri_1369, retro_itri_1398, retro_itri_1401, retro_itri_1716, retro_itri_1784, retro_itri_1846, retro_itri_220, retro_itri_285, retro_itri_526, retro_itri_606, retro_itri_688, retro_itri_702, retro_itri_977,
Ictidomys tridecemlineatus	ENSSTOG00000012168	1 retrocopy	retro_itri_1597 ,
Tupaia belangeri	ENSTBEG00000013185	6 retrocopies	retro_tbel_1861, retro_tbel_1920, retro_tbel_1996, retro_tbel_2954, retro_tbel_3209, retro_tbel_3867,
Tarsius syrichta	ENSTSYG00000006338	3 retrocopies	retro_tsyr_1574, retro_tsyr_2154, retro_tsyr_888,