RetrogeneDB ID: retro_ggor_2140

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:182960171..182960627(-)
• Located in intron of: ENSGGOG00000002766

Retrocopy information

• Ensembl ID: ENSGGOG00000022063
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2N
• Ensembl ID: ENSGGOG00000024332
• Aliases: None
• Description: None

Sequence

>retro_ggor_2140
ATGGCTGGGCTGCCTGGCAGGATCGTCAAGGAAACCCAGCGTTTGCTGGCAGAACCAGTTCCTGGCCTCAAAGCAGAACC
ATCTGAGAGCAACACCCATTATTTTCATGTGGTCATTGCCAGTCCCTGGGATTCCCACTTTGAGGGAGGGACTTTTAAAC
TTGGACCATTTCTTCCAGAAGAATACCCAATGGCAGCCCCTAAAGTGCGTTTTATGACCAAAATTTGTCATCCTAATGTA
GACAAGTTGGGGAGAATATGTTAAATACTTTGAAAGGTAAGTGGTCCCCAGCGCTGCAGATCCGCACAGTTCTGCTATGG
ATCCAGGCCTTGTTAAGTGCTCCAAATCCAGATGATCCATTAGCAAATGATGCAGAGGAGCAGTGGAAACACCAATGAAG
CTCAAGCCACACAAACAGCTAGAGCAGGGACTAGGCTATATGCCATGAATAATATT

Alignment

ORF - retro_ggor_2140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGLPRRIIXETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVR
          MAGLP.RI..ETQRLLAEPVPG.KAEP.ESN..YFHVVIA.P.DS.FEGGTFKL..FLPEEYPMAAPKVR
Retrocopy MAGLPGRIVKETQRLLAEPVPGLKAEPSESNTHYFHVVIASPWDSHFEGGTFKLGPFLPEEYPMAAPKVR

Parental  FMTKIYHPNVDKLGRIC-LDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWK-TNEAQAIE
          FMTKI.HPNVDKLGRIC.L..LK.KWSPALQIRTVLL.IQALLSAPNPDDPLAND..EQWK.TNEAQA..
Retrocopy FMTKICHPNVDKLGRIC<LNTLKGKWSPALQIRTVLLWIQALLSAPNPDDPLANDAEEQWK>TNEAQATQ

Parental  TARAWTRLYAMNNI
          TARA.TRLYAMNNI
Retrocopy TARAGTRLYAMNNI

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	0.00 RPM	62.82 RPM
SRP007412_cerebellum	0.00 RPM	42.16 RPM
SRP007412_heart	0.00 RPM	9.22 RPM
SRP007412_kidney	0.00 RPM	36.96 RPM
SRP007412_liver	0.00 RPM	22.63 RPM
SRP007412_testis	0.00 RPM	220.25 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_2140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2140 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Gorilla gorilla	ENSGGOG00000024332	4 retrocopies	retro_ggor_1079, retro_ggor_2140 , retro_ggor_2720, retro_ggor_2969,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Pteropus vampyrus	ENSPVAG00000013734	2 retrocopies	retro_pvam_1420, retro_pvam_358,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,