RetrogeneDB ID: retro_itri_1520

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393522.1:221374..221775(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRP36
• Ensembl ID: ENSSTOG00000009511
• Aliases: None
• Description: ribosomal RNA processing 36 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21374]

Sequence

>retro_itri_1520
GACCCCCGCTTTGATGATCTGTCAGGGGAATATAATCCTGAGGTGTTTGACAAAACATATTAATTCTTAAATGACATGGC
CAAAGAGAAGGAGCTTGTGAAAAAACAGTTGAAGAAGCACCTTTCAGGGGAGGAGCATGAGAAACTGCAGCAGCTGCTTC
AGCGAATGGAACAGCAAGAAATGGCACAGCAGGAGCTTCGCCCGGCCCTGAAGCTGGGGCGGCGGACTCAAGCCCAGCAG
GGTCATCGACCATACTTCCTGAAGAAATCTAACAGCGTCAGTTGGTCCTAGCTGAGAAGTTCAAGGAGCTGAAGCGCAGC
AAGAAGCTGGAGAGTTTCTTGAGTCGAAAGAGGTACCGAAATGCAGGCAAGGACAAGAGACATCTCCCTTTGAGCAGAGA
G

Alignment

ORF - retro_itri_1520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.28 %
• Parental protein coverage: 64.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DPRFDDLSGEYNPEVFDKTYQFLNDIRAKEKELVKKQLKKRLSGEEHEKLQQLLQRMEQQEMAQQERKRQ
          DPRFDDLSGEYNPEVFDKTY.FLND..AKEKELVKKQLKK.LSGEEH.....L.Q.....E...Q....Q
Retrocopy DPRFDDLSGEYNPEVFDKTY*FLNDM-AKEKELVKKQLKKHLSGEEH---EKLQQLLQRME---QQEMAQ

Parental  QELRLALKQERRTQAQQGHRPYFLKKSE-QRQLVLAEKFKELKRSKKLESFLSRKRHRNAGKDKRHLPLS
          QELR.ALK..RRTQAQQGHRPYFLKKS..QRQLVLAEKFKELKRSKKLESFLSRKR.RNAGKDKRHLPLS
Retrocopy QELRPALKLGRRTQAQQGHRPYFLKKSN<QRQLVLAEKFKELKRSKKLESFLSRKRYRNAGKDKRHLPLS

Parental  RE
          RE
Retrocopy RE

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_1520 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1520 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012525	1 retrocopy	retro_chof_160,
Otolemur garnettii	ENSOGAG00000012699	1 retrocopy	retro_ogar_3139,
Ictidomys tridecemlineatus	ENSSTOG00000009511	1 retrocopy	retro_itri_1520 ,