RetrogeneDB ID: retro_dord_357

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_13609:17157..17622(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2l3
• Ensembl ID: ENSDORG00000011406
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2L 3 [Source:MGI Symbol;Acc:MGI:109240]

Sequence

>retro_dord_357
ATGGCAGCCAGCAGGAGGCTGATGAAGGAGCTTGAAAGAGATCTGAAAATGTGGAATGAAAAACTTCCATAACATCCAGG
TTGATGAAGCTAATTTATTGACTTGGCAAGGACTTAGTGTTCCTGATAACCCTCCCTATGATCAGGGGGCCTTCAGAATT
GAAATCAACTTTCCAGCAGAGTACCCATTCAAACCACCGAAGATCATATTTAAAACAAAGATCTATCACCCCAACGTTGA
TGAAAAAGGGCAGGTCTTGTCTGCCCATCGTTAGTGCTGAGAACTGGAAGCCAGCAACCAAGACTGACCAAGTAATCCAG
TCCCTCATAGCACTGGTGAACAACCCCCCAGCCCGAGCACACCCTCTGGGCTGACCTAGCTGAAGAATACTCTAAGGACT
GTAAAAAATTCTGTAAGAACGCTGAAGAGTTTACAAAGAAAAATGGGGAAAAGTGACCTGTGGAC

Alignment

ORF - retro_dord_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASRRLMKELE-EIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKIT
          MAASRRLMKELE.EI.KCGMKNF.NIQVDEANLLTWQGL.VPDNPPYD.GAFRIEINFPAEYPFKPPKI.
Retrocopy MAASRRLMKELE>EI*KCGMKNFHNIQVDEANLLTWQGLSVPDNPPYDQGAFRIEINFPAEYPFKPPKII

Parental  FKTKIYHPNIDEKGQV-CLPVISAENWKPATKTDQVIQSLIALMND-PQLEHPLRADLAEERKK----FC
          FKTKIYHPN.DEKGQV.CLP..SAENWKPATKTDQVIQSLIAL.N..PQ.EH.L.ADLAEE..K....FC
Retrocopy FKTKIYHPNVDEKGQV>CLPIVSAENWKPATKTDQVIQSLIALVNN>PQPEHTLWADLAEEYSKDCKKFC

Parental  KNAEEFTKKYEEKQPVD
          KNAEEFTKK..EK.PVD
Retrocopy KNAEEFTKKNGEK*PVD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_357 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015284	1 retrocopy	retro_cfam_1090,
Callithrix jacchus	ENSCJAG00000015818	9 retrocopies	retro_cjac_1813, retro_cjac_1815, retro_cjac_1998, retro_cjac_2073, retro_cjac_2511, retro_cjac_2576, retro_cjac_2856, retro_cjac_3174, retro_cjac_3296,
Dipodomys ordii	ENSDORG00000006762	2 retrocopies	retro_dord_172, retro_dord_323,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Dipodomys ordii	ENSDORG00000011406	1 retrocopy	retro_dord_357 ,
Dipodomys ordii	ENSDORG00000015441	1 retrocopy	retro_dord_785,
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Gorilla gorilla	ENSGGOG00000028073	3 retrocopies	retro_ggor_1425, retro_ggor_861, retro_ggor_924,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Monodelphis domestica	ENSMODG00000017665	2 retrocopies	retro_mdom_2029, retro_mdom_956,
Mus musculus	ENSMUSG00000038965	10 retrocopies	retro_mmus_1619, retro_mmus_1620, retro_mmus_2147, retro_mmus_2212, retro_mmus_2272, retro_mmus_2315, retro_mmus_3205, retro_mmus_3714, retro_mmus_541, retro_mmus_995,
Nomascus leucogenys	ENSNLEG00000000192	1 retrocopy	retro_nleu_97,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,