RetrogeneDB ID: retro_itri_1331

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393443.1:2678748..2679584(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000027180
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GMPR2
• Ensembl ID: ENSSTOG00000002336
• Aliases: None
• Description: guanosine monophosphate reductase 2 [Source:HGNC Symbol;Acc:4377]

Sequence

>retro_itri_1331
ATGCCTCATATCGACAATGACGTGAAACTAGACTTCAAGGATGTTCTTTTGAGGCCAAAACGCAGCACCCTAAAGTCTCG
AAGTGAGGTGGATCTCACAAGATCCTTTTCATTTCGCAATTCAAAGCAGATGTACAATGGCGTCCCGATCATTGCTGCTA
ATATGGATACTGTAGGCACCTTTGAAATGGCCAAGGTTCTTTGTAAGTTCTCCCTCTTCACTGCTGTCCATAAACATTAC
AGTCTTCATCAGTGGCAAGAGTTTGCTGGCCAGAATCCTGATTGTCTTCAGTATCTGGCTGCCAGTTCAGGGACAGGCTC
TTCTGACTTTGAGCAACTGGAACAGATCCTGGAAGCTATTCCCCAGGTGAAATATATCTGCCTAGATGTGGCAATGGCTA
CTCTGAACACTTTGTTGAATTTGTAAAGGATGTACGGAAGTGCTTCCCTCAACACACCATCATGGCAGGGAATGTGGTCA
CAGGAGAGATGGTGGAAGAGTTGATCCTCTCTGGGGCTGACATCATCAAAGTGGGAATTGGGCCAGGCTCTGTGTGTACA
ACCCGGAAGAAAACTGGAGTGGGGTATCCACAGCTCAGTGCAGTGATGGAGTGTGCAGATGTTGCTCATGGCCTCAAAGG
CCACATCATTTCAGATGGAGGTTGCAGCTGCCCTGGGGATGTGGCCAAAGCTTTTGGGGCAGGGGCTGACTTTGTGATGC
TCGGTGGCATGCTGGCTGGGCACAGTGAGTCAGGTGGTGAGCTCATCGAGAGGGATGGCAAGAAGTACAAACTCTTCTAT
GGAATGAGTTCTGAAATGGCCATGAAGAAGTACGCT

Alignment

ORF - retro_itri_1331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.57 %
• Parental protein coverage: 82.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPHIDNDVKLDFKDVLLRPKRSTLKSRSEVDLTRSFSFRNSKQMYNGVPIIAANMDTVGTFEMAKVLCKF
          MPHIDNDVKLDFKDVLLRPKRSTLKSRSEVDLTRSFSFRNSKQMYNGVPIIAANMDTVGTFEMAKVLCKF
Retrocopy MPHIDNDVKLDFKDVLLRPKRSTLKSRSEVDLTRSFSFRNSKQMYNGVPIIAANMDTVGTFEMAKVLCKF

Parental  SLFTAVHKHYSLHQWQEFAGQNPDCLQYLAASSGTGSSDFEQLEQILEAIPQVKYICLDVA-NGYSEHFV
          SLFTAVHKHYSLHQWQEFAGQNPDCLQYLAASSGTGSSDFEQLEQILEAIPQVKYICLDVA.NGYSEHFV
Retrocopy SLFTAVHKHYSLHQWQEFAGQNPDCLQYLAASSGTGSSDFEQLEQILEAIPQVKYICLDVA<NGYSEHFV

Parental  EFVKDVRKRFPQHTIMAGNVVTGEMVEELILSGADIIKVGIGPGSVCTTRKKTGVGYPQLSAVMECADAA
          EFVKDVRK.FPQHTIMAGNVVTGEMVEELILSGADIIKVGIGPGSVCTTRKKTGVGYPQLSAVMECAD.A
Retrocopy EFVKDVRKCFPQHTIMAGNVVTGEMVEELILSGADIIKVGIGPGSVCTTRKKTGVGYPQLSAVMECADVA

Parental  HGLKGHIISDGGCSCPGDVAKAFGAGADFVMLGGMLAGHSESGGELIERDGKKYKLFYGMSSEMAMKKWA
          HGLKGHIISDGGCSCPGDVAKAFGAGADFVMLGGMLAGHSESGGELIERDGKKYKLFYGMSSEMAMKK.A
Retrocopy HGLKGHIISDGGCSCPGDVAKAFGAGADFVMLGGMLAGHSESGGELIERDGKKYKLFYGMSSEMAMKKYA

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_1331 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1331 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001231	1 retrocopy	retro_chof_1628,
Echinops telfairi	ENSETEG00000018395	1 retrocopy	retro_etel_373,
Microcebus murinus	ENSMICG00000001736	1 retrocopy	retro_mmur_1510,
Otolemur garnettii	ENSOGAG00000016593	1 retrocopy	retro_ogar_623,
Ictidomys tridecemlineatus	ENSSTOG00000002336	1 retrocopy	retro_itri_1331 ,