RetrogeneDB ID: retro_ptro_489

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:62016753..62017271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL35
• Ensembl ID: ENSPTRG00000012152
• Aliases: None
• Description: mitochondrial ribosomal protein L35 [Source:HGNC Symbol;Acc:14489]

Sequence

>retro_ptro_489
ATGGCTGCTTTTGCCTTTGCTGGTGCAGTGAGAGCAGCTTCAGGAATCCGATGGCTCTTGAATATTTTGGCATCTTCAGC
CTACAGAAACTGTGTCAAGAATGCCTCTCTTATTTCTGCATTGTCCACTGGACGTTTTAGTCATATTTAGACACCAGTTG
TTTCCTCCACTCCCAGACTTAACCACATCTGAGAGAAACCTGACATGTGGGCATACTTCAGCGATCCTTAATAGAGTGTC
CCCCTTGCTTCCGAGTGTCCTGAAGCTGCCAGTCAGATCTCTAACATACTTCAGTACATGAAAAGACAAGAGAAAGACTG
TGAAAGCTGTCATCTACAGGTTTCTTTGACTTCATTGTGGCCTTTGGGTGAGGTGAAAGGCTGGTTAAAAGAAAAAATTA
TGGAAAAAGGAAACTGCAAGAAAAAAGCGATTGAGGGAATTTGTATTCTGCAATAAAACCCAGAGTAAACTCTTAAGATA
AAATGGTGACGTCATTCTGGGAGAGGTAAAACTGGTAT

Alignment

ORF - retro_ptro_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 97.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPR-LTTSERNLTC
          MAA.AFAGAVRAASGI...LNILASS.YRNCVKNASLISALSTGRFSHI.TPVVSSTPR.LTTSERNLTC
Retrocopy MAAFAFAGAVRAASGIRWLLNILASSAYRNCVKNASLISALSTGRFSHI*TPVVSSTPR>LTTSERNLTC

Parental  GHTSAILNRVAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCGLWVRRKAGYKKKLWKKTPA
          GHTSAILNRV.P.LPSVLKLPVRSLTYFS..K.KRKTVKAVI.RFL.LHCGLWVR.KAG...........
Retrocopy GHTSAILNRVSPLLPSVLKLPVRSLTYFST*KDKRKTVKAVIYRFL*LHCGLWVR*KAGXXXXXXXXXXX

Parental  RKKRLREFVFCNKTQSKLL-DKMTTSFWKRRNWH
          ...RLREFVFCNKTQSKLL.DKM.TSFW.R.NW.
Retrocopy XXXRLREFVFCNKTQSKLL>DKMVTSFWER*NWY

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	0.04 RPM	7.44 RPM
SRP007412_cerebellum	0.04 RPM	5.56 RPM
SRP007412_heart	0.03 RPM	16.03 RPM
SRP007412_kidney	0.00 RPM	9.94 RPM
SRP007412_liver	0.00 RPM	5.30 RPM
SRP007412_testis	0.00 RPM	2.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_489 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_489 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_681
Pongo abelii	retro_pabe_541

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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,