RetrogeneDB ID: retro_itri_101

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393314.1:5914208..5915249(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023821
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000001481
• Aliases: None
• Description: None

Sequence

>retro_itri_101
ATGGTCGGCGGCGGTGGCAAGCGCAGGCCCACTAGGGAGGGGCAGCAGTGTGAAAAAGCAGTTGATGTGAAGAAGAGTAA
ATCCTGTGAAGCTGATGTCTCTAGTGACCTTCGCAAAGAAGTAGAAGATCATTATAAGCTTTTCCTACCTGAAGATTTCT
ATCACTTCTGGAAGTTTTGTGAAGAACTTGATCCTGAAAAGCCAGCTGATTCACTTTCCACAAGTCTTGGACTTCGATTA
GTGGGTCCGTATGATATTCTGGCTGGAAAACATAAAATGAAGAAAAAATCATTAGGTTTGAACTTTAATCTTCACCGGAG
GTTTTACTATGATCCTCCTGAGTTCCAGACCATTATTATTGGCGATAATAAAACTCAGTACCACATGGGGTATTTCAGGG
ATTCTCCTGATGAACTGCCTGTATATGTCGGTATAAATGAAGCAAAGAAAAATTGTACAATTATTCAAAATGGAGATAAT
GTGTTTGCTGCAGTCAAATTATTTTTGATGAAAAAACTTAAAGAAGTAACAGATAAAAAGAAAGCTAGTCTGTTGAAAAA
CGTAGATGAAAAACTCACAGAAGCAGCCAGAAAACTGGGGTACTCACTTGAACAGAGAACCCTGAAGATGAAACAGAGAG
ATAAGAAAGTCGTGACAAAGACCTTTCACAGTGCAGGTTTGGTTGTTCCAGTAGATAAAAATGATGTTGGGTACAGAGAG
CTCCCCGAAACAGATGCTGACCTCAAGACAATTTGCAAGACAATTGTTGAGGCTGCAAGTGATGAGGAGAGACTGAAAGC
ATTCGCTCCCATTCAGGAAATGATGACTTTTGTGCAGTTTGCCAATGATGAGTGTGATTATGGCATGGGGCTAGAGCTGG
GAATGGACCTCTTTTGCTATGGTTCACACTATTTTCATAAAGTAGCTGGCCAGCTTTTACCTCTTGCATATAATCTGTTG
AAGAGGAATCTGTTTGCAGAAATTATTGAAGATCATCTGGCAAACAGAAGTAAAGAGAACGTAGACCAACTTGCAGGATG
A

Alignment

ORF - retro_itri_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.97 %
• Parental protein coverage: 99.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGGGKRRPAREGQQCEKAVDVKKSKSCEADVSSDLRKEVENHYKLSLPEDFYHFWKFCEELDPEKPADSL
          GGGGKRRP.REGQQCEKAVDVKKSKSCEADVSSDLRKEVE.HYKL.LPEDFYHFWKFCEELDPEKPADSL
Retrocopy GGGGKRRPTREGQQCEKAVDVKKSKSCEADVSSDLRKEVEDHYKLFLPEDFYHFWKFCEELDPEKPADSL

Parental  STSLGLRLVGPYDILAGKHKMKKKSLGLNFNLHWRFYYDPPEFQTIIIGDNKTQYHMGYFRDSPDELPVY
          STSLGLRLVGPYDILAGKHKMKKKSLGLNFNLH.RFYYDPPEFQTIIIGDNKTQYHMGYFRDSPDELPVY
Retrocopy STSLGLRLVGPYDILAGKHKMKKKSLGLNFNLHRRFYYDPPEFQTIIIGDNKTQYHMGYFRDSPDELPVY

Parental  VGINEAKKNCTIVQNGDNVFAAVKLFVMKKLKEVTDKKKASLLKNVDEKLTEAARKLGYSLEQRTLKMKQ
          VGINEAKKNCTI.QNGDNVFAAVKLF.MKKLKEVTDKKKASLLKNVDEKLTEAARKLGYSLEQRTLKMKQ
Retrocopy VGINEAKKNCTIIQNGDNVFAAVKLFLMKKLKEVTDKKKASLLKNVDEKLTEAARKLGYSLEQRTLKMKQ

Parental  RDKKVVTKTFHSAGLVVPVDKNDVGYRELPETDADLKRICKTIVEAASDEERLKAFAPIQEMMTFVQFAN
          RDKKVVTKTFHSAGLVVPVDKNDVGYRELPETDADLK.ICKTIVEAASDEERLKAFAPIQEMMTFVQFAN
Retrocopy RDKKVVTKTFHSAGLVVPVDKNDVGYRELPETDADLKTICKTIVEAASDEERLKAFAPIQEMMTFVQFAN

Parental  DECDYGMGLELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRNLFAEIIEDHLANRSKENVDQLAG
          DECDYGMGLELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRNLFAEIIEDHLANRSKENVDQLAG
Retrocopy DECDYGMGLELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRNLFAEIIEDHLANRSKENVDQLAG

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_101 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_101 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020132	1 retrocopy	retro_btau_611,
Equus caballus	ENSECAG00000013735	1 retrocopy	retro_ecab_551,
Gorilla gorilla	ENSGGOG00000003090	1 retrocopy	retro_ggor_2306,
Myotis lucifugus	ENSMLUG00000017052	1 retrocopy	retro_mluc_395,
Otolemur garnettii	ENSOGAG00000008007	1 retrocopy	retro_ogar_807,
Ictidomys tridecemlineatus	ENSSTOG00000001481	1 retrocopy	retro_itri_101 ,
Tursiops truncatus	ENSTTRG00000009751	1 retrocopy	retro_ttru_862,