RetrogeneDB ID: retro_ggor_1425

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:9969724..9970161(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSGGOG00000028073
• Aliases: None
• Description: None

Sequence

>retro_ggor_1425
GAAGAGCTTGAGGAAATTGCAAATGTGGGATGAAAAACTTCCCGTAACATCCAGGTTGATGAAGCTAATTTATTGACTTA
GCAAGGGCTTATTGTTCCTGACAACTCTCCATATGATTAGGTGACCTTCAGAATCGAAATCAACTTTCCAGCAGAGTACC
CATTCAAACTACCAAAGATCACATTTAAAACAAAGATCTATCCCCCAAATATCGACGAAAAGGGGCAGGTCTGTCTGTCA
GTAATTAGTGCTGAAAACTGGAAGCCAGCAACCAAAACCGACCAAGTAATCCAGTCCCTCACAGCACTGGTGAATGACCC
CCAGCCCGAGCACCCGCTTCGGGCTGACCTAGCTGAAGAATACTCTAAGGACTGTAAAAAATTCTGTAAGAATGCTGAAG
AGTTTACAAAGAAATATGGGGAAAGTGACCTGTGGAC

Alignment

ORF - retro_ggor_1425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KELEEIR-KCGMKNF-RNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYH
          .ELEEI..KCGMKNF.RNIQVDEANLLT.QGLIVPDN.PYD...FRIEINFPAEYPFK.PKITFKTKIY.
Retrocopy EELEEIA<KCGMKNF>RNIQVDEANLLT*QGLIVPDNSPYD*VTFRIEINFPAEYPFKLPKITFKTKIYP

Parental  PNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNAEEFTKK
          PNIDEKGQVCL.VISAENWKPATKTDQVIQSL.ALVNDPQPEHPLRADLAEEYSKD.KKFCKNAEEFTKK
Retrocopy PNIDEKGQVCLSVISAENWKPATKTDQVIQSLTALVNDPQPEHPLRADLAEEYSKDCKKFCKNAEEFTKK

Parental  YGE-KRPVD
          YGE.K.PVD
Retrocopy YGE<K*PVD

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	0.38 RPM	79.94 RPM
SRP007412_cerebellum	1.06 RPM	76.16 RPM
SRP007412_heart	0.09 RPM	22.11 RPM
SRP007412_kidney	0.61 RPM	60.97 RPM
SRP007412_liver	0.21 RPM	32.34 RPM
SRP007412_testis	0.21 RPM	61.33 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1425 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 41 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	ENSDORG00000011406	1 retrocopy	retro_dord_357,
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843, retro_ggor_2936, retro_ggor_436,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Gorilla gorilla	ENSGGOG00000010832	1 retrocopy	retro_ggor_953,
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,