RetrogeneDB ID: retro_itri_28

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:9519465..9520281(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019847
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000007466
• Aliases: None
• Description: None

Sequence

>retro_itri_28
ATGCTGCAGCTGCGGGACTCGGTGGACTCCGCGGGCACGAGCCCCACGACCCTGCTGGCGGCCGGCGAGGATGTGGGGCC
GGGCAGCGCAGGCGGGGCCCGGGCAGGGGTGGGCACGCCACTGCGCCAGACGCTGTGGCCGCTCAGCGTCCACGACCCCA
CGCGCCGCGCCCGCGTCAAGGAGTACTTCGTGTTCCGGCCCGGCACCATCGAGCAGGCCGTGGAAGAGATCCGCGCCGTT
GTCCGGCCCGTGGAGGACGGCGAGATCCAGGGGGTGTGGCTGCTGACCGAGGTGGACCACTGGAACAACGAAAAAGAGCG
TCTGGTGTTGGTCACTGACCAGTCGTTGCTCATCTGTAAGTACGACTTCATCAGCCTTCAGTGCCAGCAGGTGGTCAGGG
TGGCACTCAGTGCAGTGGACACCATCTCCCACGGAGAGTTCCAGTTTCCCCCCAAATCTCTCAACAAGCGAGAAGGCTTT
GGGATTCGCATCCAATGGGACAAGCAGAGTCGTCCTTCTTTCATAAACAGATGGAACCCCTGGTCCACAAACGTGCCCTA
CGCCACTTTCATAGAGCACCCAATGGCTGGTGTGGATGAAAAGACGGCTTCTCTGTGCCAGTTGGAAAGCTTCAAGGCTC
TGTTAATCCAAGCTGTCAAAAAAGCCCAAAAAGAAAGTCCTCTGCCAGGACAAGCGAATGGTGTGCTGGTCTTGGAGCGG
CCCCTGCTCATCGAGACCTACGTGGGATTGATGTCCTTCATCAACAACGAGGCCAAACTGGGTTATTCCATGACCAGAGG
CAAGATTGGCTTCTAG

Alignment

ORF - retro_itri_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLQLRDSVDSAGTSPTALLAAGEDVGPGSAGGARAGVGTPLRQTLWPLSVHDPTRRARVKEYFVFRPGTI
          MLQLRDSVDSAGTSPT.LLAAGEDVGPGSAGGARAGVGTPLRQTLWPLSVHDPTRRARVKEYFVFRPGTI
Retrocopy MLQLRDSVDSAGTSPTTLLAAGEDVGPGSAGGARAGVGTPLRQTLWPLSVHDPTRRARVKEYFVFRPGTI

Parental  EQAVEEIRAVVRPVEDGEIQGVWLLTEVDHWNNEKERLVLVTDQSLLICKYDFISLQCQQVVRVALSAVD
          EQAVEEIRAVVRPVEDGEIQGVWLLTEVDHWNNEKERLVLVTDQSLLICKYDFISLQCQQVVRVALSAVD
Retrocopy EQAVEEIRAVVRPVEDGEIQGVWLLTEVDHWNNEKERLVLVTDQSLLICKYDFISLQCQQVVRVALSAVD

Parental  TISHGEFQFPPKSLNKREGFGIRIQWDKQSRPSFINRWNPWSTNVPYATFIEHPMAGVDEKTASLCQLES
          TISHGEFQFPPKSLNKREGFGIRIQWDKQSRPSFINRWNPWSTNVPYATFIEHPMAGVDEKTASLCQLES
Retrocopy TISHGEFQFPPKSLNKREGFGIRIQWDKQSRPSFINRWNPWSTNVPYATFIEHPMAGVDEKTASLCQLES

Parental  FKALLIQAVKKAQKESPLPGQANGVLVLERPLLIETYVGLMSFINNEAKLGYSMTRGKIGF
          FKALLIQAVKKAQKESPLPGQANGVLVLERPLLIETYVGLMSFINNEAKLGYSMTRGKIGF
Retrocopy FKALLIQAVKKAQKESPLPGQANGVLVLERPLLIETYVGLMSFINNEAKLGYSMTRGKIGF

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_28 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_28 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006651	1 retrocopy	retro_mdom_1017,
Pteropus vampyrus	ENSPVAG00000015273	1 retrocopy	retro_pvam_1018,
Ictidomys tridecemlineatus	ENSSTOG00000007466	1 retrocopy	retro_itri_28 ,
Tupaia belangeri	ENSTBEG00000011399	7 retrocopies	retro_tbel_1982, retro_tbel_2169, retro_tbel_2300, retro_tbel_2302, retro_tbel_2339, retro_tbel_2599, retro_tbel_2603,