RetrogeneDB ID: retro_ggor_2979

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:12743466..12744029(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL35
• Ensembl ID: ENSGGOG00000026769
• Aliases: None
• Description: None

Sequence

>retro_ggor_2979
ATGGCTTCCTCTGCCTTTGCTGGTGCGATGAGAGCAGCTTCAGGAATCTATGGCTCCTGAATATTTTTGCATCTCCAACC
CACCGAAACTGTGCCAGGAATGCCTCTCTTATTTCTGCATTCTCTACTGGACGTTTTAGTCATATTCGGACACCATTTGT
TTCCTCCACTCCCAGGCTTATCACATCTGTCAGAAACCTGACATGTGGGCATACTGCAGTGTTCCCCAACAGAGTGGCCC
CCTTGCTTCCAAGTGTCCTGAAGCTGCCAGTCAGAACTGTAATATACGTCAGTACACAAAAAGGCAAGAGAAAAACTGTG
AAAGCTGTTATCTATAGGTTTTTTCGACTTCATTCTGGCCTTTGGGTGAGGAGAAAGGCTAGTTATAAGAAAAAATTCTG
GAAAAAGACACCTGCAAGAGAAAAGCAATTGAGGGAATTTGTGTTCTGCAATAAAACCCAGAGTAAACTCTTAGATAAAA
TGACAGTGTCCTTCTGGAAGAGGTGAAACTTGTATGCTGATAATCCTTATCAGAAATATCTTTATGAAACAAACCTGAAA
GTA

Alignment

ORF - retro_ggor_2979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASAFAGAVRAASGI-LRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRLTTSERNLTC
          MA.SAFAGA.RAASGI.L..LNI.AS.T.RNC..NASLISA.STGRFSHI.TP.VSSTPRL.TS.RNLTC
Retrocopy MASSAFAGAMRAASGI<LWLLNIFASPTHRNCARNASLISAFSTGRFSHIRTPFVSSTPRLITSVRNLTC

Parental  GHTSAILNRVAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCGLWVRRKAGYKKKLWKKTPA
          GHT....NRVAP.LPSVLKLPVR...Y.S..KGKRKTVKAVI.RF.RLH.GLWVRRKA.YKKK.WKKTPA
Retrocopy GHTAVFPNRVAPLLPSVLKLPVRTVIYVSTQKGKRKTVKAVIYRFFRLHSGLWVRRKASYKKKFWKKTPA

Parental  RKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKYHDRTNLKV
          R.K.LREFVFCNKTQSKLLDKMT.SFWKR.N.Y.D.PYQKY...TNLKV
Retrocopy REKQLREFVFCNKTQSKLLDKMTVSFWKR*NLYADNPYQKYLYETNLKV

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	53.13 RPM
SRP007412_cerebellum	0.00 RPM	33.17 RPM
SRP007412_heart	0.00 RPM	20.29 RPM
SRP007412_kidney	0.00 RPM	29.36 RPM
SRP007412_liver	0.00 RPM	16.06 RPM
SRP007412_testis	0.00 RPM	18.13 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_2979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2979 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4784
Pan troglodytes	retro_ptro_3185
Pongo abelii	retro_pabe_3724

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019467	1 retrocopy	retro_cjac_203,
Dasypus novemcinctus	ENSDNOG00000008329	1 retrocopy	retro_dnov_404,
Homo sapiens	ENSG00000132313	4 retrocopies	retro_hsap_3424, retro_hsap_4784, retro_hsap_595, retro_hsap_681,
Gorilla gorilla	ENSGGOG00000026769	3 retrocopies	retro_ggor_2315, retro_ggor_2979 , retro_ggor_526,
Macropus eugenii	ENSMEUG00000004773	1 retrocopy	retro_meug_1703,
Mus musculus	ENSMUSG00000052962	1 retrocopy	retro_mmus_1777,
Otolemur garnettii	ENSOGAG00000004048	1 retrocopy	retro_ogar_2600,
Pan troglodytes	ENSPTRG00000012152	4 retrocopies	retro_ptro_2325, retro_ptro_3185, retro_ptro_438, retro_ptro_489,
Rattus norvegicus	ENSRNOG00000008546	1 retrocopy	retro_rnor_1399,
Tupaia belangeri	ENSTBEG00000015366	10 retrocopies	retro_tbel_1143, retro_tbel_146, retro_tbel_2647, retro_tbel_289, retro_tbel_2892, retro_tbel_3789, retro_tbel_3828, retro_tbel_428, retro_tbel_4379, retro_tbel_627,
Tarsius syrichta	ENSTSYG00000007713	2 retrocopies	retro_tsyr_1128, retro_tsyr_264,