RetrogeneDB ID: retro_itri_2

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393348.1:5650524..5652201(-)
• Located in intron of: ENSSTOG00000014276

Retrocopy information

• Ensembl ID: ENSSTOG00000027430
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000027666
• Aliases: None
• Description: None

Sequence

>retro_itri_2
GCCTTGAAGAGGTCCTTCGAGGTCGGGGAGGCCGAGCCACCCAACTCAACCCCGCCCCGGCGGGTCCAGACGCCCCTGCT
CCGGGCCACTGTGGCCAGCTCCACCCAGAAGTTCCAGGACCTGGGTGTGAAGAACTCAGAGCCCTCCGCCCGCCATGTAG
ACCCCCTGGGCCAGCGCTCGCCCAAGCCTGCCCTGCGGAGGGTGGAGCTCGCGGGGTCCAAGGTGCCTGAACCCGTGTCC
CGCCGCACGGAGCTCTCCATCGACATCTCGTCCAAGCAGGTGGAGAGCGCGGCCACCCCTGGGCCGGCCCGGTTCGGGCT
CAAGAGGGCCGAGGCGCTGGGCCACAAGACCCCAGACCCGACCCCTCGGAGGACGGAGGTCACCATCGTCAAGCCCCCGG
AGCCAGCCCACCGCAGGATGGAGGCCCCTGCCTCCAAGACCCCCGAGGTGCCTGCCAGCCCTGCCGTCGACGCAGCCCCC
AAGAGGGTGGAGATCCAGGTGCCCAAGCCGGCCGAGGCGCCCGCCTGTCCCCTCCCACCCCAGACCCTGGAGAATTCAGA
GCCTGCCCTGACGTCCCAGCTGCAGAGCAGGCTGGAGCCCAAGCCCCCGCTGGCCGAGGCCCTGCCCAGGAGCCCCGAGG
TCCCCGAGGCAGCTCCCCGCAGCGCTGGCAACATGGCCGACTCCTCCAGGGATGCCGCCCTCAAGCAGGCCGCGGCCACG
CGGAACGAGAAGGCCCCCGTGGAGTTCGGCTACGTGGGCATCGACTCCATCCTGGAGCAGATGCGGAGGAAGGCCATGAA
GCAGGGCTTCGAGTTCAACATCATGGTGGTGGGGCAGAGCGGCCTGGGGAAGTCCACCTTAATCAACACCCTCTTCAAAT
CCAAGATCAGCCGGAAGTCGGTGCAGCCCCCCTCGGAGGAGCGCATCCCCAAGACCATCGAGATCAAGTCCATCACACAC
GATATCGAGGAGAAGGGCGTCCGGATGAAGCTGACGGTAATCGACACGCCGGGCTTTGGGGACCACATCAATAACGAGAA
CTGCTGGCAGCCGATCATGAAGTTCATCAACGAACAGTACGAGAAGTACTTGCAGGAGGAGGTCAACATCAACCGGAAGA
AGCGCATCCCGGACACGCGCGTCCACTGCTGCCTCTACTTCATCCCTGCCACGGGCCACTCCCTCAGGCCCCTGGACATC
GAGTTCATGAAGCGCCTAAGCAAGGTGGTCAACATCGTCCCCGTCATTGCCAAGGCTGACACACTGACCCTGGAGGAGAG
GGTCTACTTCAAACAGCGGATCACCGCAGACCTGCTGTCCAACGGCATCGACGTGTACCCCCAGAAGGAGTTTGACGAGG
ACTCGGAGGACAGGCTGGTGAACGAGAAGTTCCGGGAGATGATCCCGTTTGCCGTGGTGGGCAGTGACCAGGAGTACCAA
GTCAATGGCAAGCGGATCCTCGGGAGGAAGACCAAGTGGGGCACCATTGAAGTCGAGAACACCACGCACTGTGAGTTTGC
CTACCTGCGGGACCTGCTCATCAGGACGCACATGCAGAACATCAAGGACATCACCAGCAGCATCCACTTCGAAGCCTACC
GTGTGAAGCGCCTCAGCGAGGGCAGCAGCACCCTGGCCAACGGGCTGGAGAAGGAGCCAGACGCTGAGGAGATGTAG

Alignment

ORF - retro_itri_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.03 %
• Parental protein coverage: 60.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALKRSFEVEEAEPPNSTPPRRVQTPLLRATVASSTQKFQDLGVKNSEPSARHVDPLGQRSPKPALRRVEL
          ALKRSFEV.EAEPPNSTPPRRVQTPLLRATVASSTQKFQDLGVKNSEPSARHVDPLGQRSPKPALRRVEL
Retrocopy ALKRSFEVGEAEPPNSTPPRRVQTPLLRATVASSTQKFQDLGVKNSEPSARHVDPLGQRSPKPALRRVEL

Parental  AGSKVPEPVSRRTELSIDISSKQVESAATPGPARFGLKRAEALGHKTPDPTPRRTEVTIVKPPEPAHRRM
          AGSKVPEPVSRRTELSIDISSKQVESAATPGPARFGLKRAEALGHKTPDPTPRRTEVTIVKPPEPAHRRM
Retrocopy AGSKVPEPVSRRTELSIDISSKQVESAATPGPARFGLKRAEALGHKTPDPTPRRTEVTIVKPPEPAHRRM

Parental  EAPASKTPEVPASPAVDTAPKRVEIQVPKPAEAPACPLPPQTLENSEPALTSQLQSRLEPKPPLAEALPR
          EAPASKTPEVPASPAVD.APKRVEIQVPKPAEAPACPLPPQTLENSEPALTSQLQSRLEPKPPLAEALPR
Retrocopy EAPASKTPEVPASPAVDAAPKRVEIQVPKPAEAPACPLPPQTLENSEPALTSQLQSRLEPKPPLAEALPR

Parental  SPEVPEAAPGSAGNMADSSRDAALKQAAATRNEKAPVEFGYVGIDSILEQMRRKAMKQGFEFNIMVVGQS
          SPEVPEAAP.SAGNMADSSRDAALKQAAATRNEKAPVEFGYVGIDSILEQMRRKAMKQGFEFNIMVVGQS
Retrocopy SPEVPEAAPRSAGNMADSSRDAALKQAAATRNEKAPVEFGYVGIDSILEQMRRKAMKQGFEFNIMVVGQS

Parental  GLGKSTLINTLFKSKISRKSVQPPSEER
          GLGKSTLINTLFKSKISRKSVQPPSEER
Retrocopy GLGKSTLINTLFKSKISRKSVQPPSEER

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_2 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_2 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000013357	1 retrocopy	retro_itri_1227,
Ictidomys tridecemlineatus	ENSSTOG00000021378	3 retrocopies	retro_itri_1332, retro_itri_1736, retro_itri_1771,
Ictidomys tridecemlineatus	ENSSTOG00000027666	1 retrocopy	retro_itri_2 ,