RetrogeneDB ID: retro_itri_1528

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393527.1:2052280..2052676(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSSTOG00000016293
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2L 3 [Source:HGNC Symbol;Acc:12488]

Sequence

>retro_itri_1528
ATGAAAAGCTTCCATTACATCCAGGTTGATGAAGCTAATTTATTGATTGGCAAAGGCTTATTGTTCCTGACAATCCTCCC
TATGATAAGGGGGCCTTCAGAATCAAAATAAACTTTTCAGCAGAATACCCATTCAAATCACCAAAGATCACATTTAAAAA
CAAAGATCTACCACCCAAACACAGATGAAAAATGGCAGGTCTGCTTGCCAGTAATTAGTGCTGAGAACTGGATGCCAGCA
ACCAAGACCAACCAAGCAATCCTGTCCCTCATAGCACCCCAGACCATGCACCTGCTCTGGGTTGACCTAATTGAAGAATT
CTCTAAGGAACGTAAAAAATTCTGTAAGAACACTGAAGAGTTTTCAAAGAAATATGGAGAAAAGTGACCTGTGGAC

Alignment

ORF - retro_itri_1528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKNFRNIQVDEANLLT-WQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFK-TKIYHPNIDEKGQVC
          MK.F..IQVDEANLL..WQ.LIVPDNPPYDKGAFRI.INF.AEYPFK.PKITFK.TKIYHPN.DEK.QVC
Retrocopy MKSFHYIQVDEANLLI<WQRLIVPDNPPYDKGAFRIKINFSAEYPFKSPKITFK>TKIYHPNTDEKWQVC

Parental  LPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD
          LPVISAENW.PATKT.Q.I.SLIA....PQ..H.L..DL.EE.SK.RKKFCKN.EEF.KKYGEK.PVD
Retrocopy LPVISAENWMPATKTNQAILSLIA----PQTMHLLWVDLIEEFSKERKKFCKNTEEFSKKYGEK*PVD

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_1528 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1528 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 14 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Homo sapiens	ENSG00000185651	4 retrocopies	retro_hsap_1094, retro_hsap_1185, retro_hsap_1338, retro_hsap_1960,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Nomascus leucogenys	ENSNLEG00000000192	1 retrocopy	retro_nleu_97,
Oryctolagus cuniculus	ENSOCUG00000002610	3 retrocopies	retro_ocun_826, retro_ocun_932, retro_ocun_937,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Pteropus vampyrus	ENSPVAG00000013575	1 retrocopy	retro_pvam_727,
Sorex araneus	ENSSARG00000005137	3 retrocopies	retro_sara_105, retro_sara_277, retro_sara_653,
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,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,