RetrogeneDB ID: retro_itri_1371

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393460.1:3649251..3649629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSSTOG00000025799
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:HGNC Symbol;Acc:12477]

Sequence

>retro_itri_1371
AGTGCTGGACCCAAAGGAGACAATATTTATGAATGGAGGTCAACTATATTGGGACCCCCTGGATCTGTCTATGAAGGAGG
GGTGTTCTTTCTTGACATTACCTTTTCACCAGACTATCCACTTAAACCCCCAAAGGTTACCTTCCGAATAAGAATCTATC
ACTGTAATATTAACAGCCAAGGTGTGATCTGTCTAGACATCCTGAAAGACAACTGGAGTCCAGCCCTAACCATCTCTAAA
GTTCTTCTCTCCATCTGCTCACTTTTTACAGAATGCAACCCTGCCGATCCTCTGGTGGGCAGCATTGCCACACAGTACAT
GACCAACAGAGCAGAGCACAACCGGATGGCCAGACAGTGGACCAAGCAGTACGCCACA

Alignment

ORF - retro_itri_1371 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKD
          SAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITF.P.YP.KPPKVTFR.RIYHCNINSQGVICLDILKD
Retrocopy SAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPLKPPKVTFRIRIYHCNINSQGVICLDILKD

Parental  NWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
          NWSPALTISKVLLSICSL.T.CNPADPLVGSIATQYMTNRAEH.RMARQWTK.YAT
Retrocopy NWSPALTISKVLLSICSLFTECNPADPLVGSIATQYMTNRAEHNRMARQWTKQYAT

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_1371 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1371 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 11 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Dipodomys ordii	ENSDORG00000015441	1 retrocopy	retro_dord_785,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Pteropus vampyrus	ENSPVAG00000001773	1 retrocopy	retro_pvam_1451,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Ictidomys tridecemlineatus	ENSSTOG00000016293	2 retrocopies	retro_itri_1528, retro_itri_655,
Ictidomys tridecemlineatus	ENSSTOG00000025799	2 retrocopies	retro_itri_1371 , retro_itri_645,