RetrogeneDB ID: retro_pabe_99

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:29949476..29949938(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005254
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSPPYG00000011602
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 L3 [Source:RefSeq peptide;Acc:NP_001127614]

Sequence

>retro_pabe_99
ATGGCGGCCAGCAGGAGGCTGATGAAGGAGCTTGAAGAAATCCGCAAATGTGGAATGGAAAACTTCCGTAACATCCAGGT
TGATGAAGCTAATTTATTGACTTGGCAAGGGCTTATTGTTCCTGACAACCCTCCGTATAATAAGGGGGCCTTCAGAATCG
AAATCAACTTTCCAGCAGAGTACCCATTCAAACCACCGAGGATCACATTTAAAACAAAGATCTATCACCCGAACATCGAC
GAAAAGGGGCAGGTCTGTCTGCCAGTAATTAGTGCTGAAAACTGGAAGCCAGCAACCAAAACCGACCAAGTAATCCAGTC
CCTCATAGCACTGGTGAATGACCCGCAGCCCGAGCATCCGCTTCGGGCTGACCTAGCTGAAGAATACTCTAAAGACCGTA
AAAAATTCTGTAAGAATGCTGAAGAGTTTACAAAGAAATATGGGGAAAAGCGACCTGTGGAC

Alignment

ORF - retro_pabe_99 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITF
          MAASRRLMKELEEIRKCGM.NFRNIQVDEANLLTWQGLIVPDNPPY.KGAFRIEINFPAEYPFKPP.ITF
Retrocopy MAASRRLMKELEEIRKCGMENFRNIQVDEANLLTWQGLIVPDNPPYNKGAFRIEINFPAEYPFKPPRITF

Parental  KTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNA
          KTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNA
Retrocopy KTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNA

Parental  EEFTKKYGEKRPVD
          EEFTKKYGEKRPVD
Retrocopy EEFTKKYGEKRPVD

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.28 RPM	77.02 RPM
SRP007412_cerebellum	0.36 RPM	69.92 RPM
SRP007412_heart	0.00 RPM	23.57 RPM
SRP007412_kidney	0.07 RPM	52.80 RPM
SRP007412_liver	0.06 RPM	32.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_99 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_99 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_99 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 62 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,
Cavia porcellus	ENSCPOG00000006044	2 retrocopies	retro_cpor_692, retro_cpor_835,
Dipodomys ordii	ENSDORG00000011406	1 retrocopy	retro_dord_357,
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Homo sapiens	ENSG00000185651	4 retrocopies	retro_hsap_1094, retro_hsap_1185, retro_hsap_1338, retro_hsap_1960,
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,
Oryctolagus cuniculus	ENSOCUG00000002610	3 retrocopies	retro_ocun_826, retro_ocun_932, retro_ocun_937,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99 ,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pongo abelii	ENSPPYG00000015844	6 retrocopies	retro_pabe_1016, retro_pabe_1164, retro_pabe_1257, retro_pabe_2330, retro_pabe_30, retro_pabe_3670,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Pteropus vampyrus	ENSPVAG00000013575	1 retrocopy	retro_pvam_727,
Rattus norvegicus	ENSRNOG00000001862	4 retrocopies	retro_rnor_1602, retro_rnor_2633, retro_rnor_2799, retro_rnor_526,
Sorex araneus	ENSSARG00000005137	3 retrocopies	retro_sara_105, retro_sara_277, retro_sara_653,
Ictidomys tridecemlineatus	ENSSTOG00000016293	2 retrocopies	retro_itri_1528, retro_itri_655,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,