RetrogeneDB ID: retro_pabe_541

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:72077743..72078253(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL35
• Ensembl ID: ENSPPYG00000012214
• Aliases: None
• Description: mitochondrial ribosomal protein L35 [Source:HGNC Symbol;Acc:14489]

Sequence

>retro_pabe_541
ATGGCTGCTTTTGCCTTTGCTGGTGCGGTGAGAGCAGCTTCAGGAATCTGATGGCCCTTGAATATTTTGGCATCTTCAGC
CTACCAAAACTGTGTCAAGAATGCCTCTCTTATTTCTGCATTGTCCACTGGACGTTTTAGTCATATTCAGACACCAGTTG
TTTCCTCCACTCCCAGACTTACCACATCTGAGAGAAACCTGACATGTGGGCATACTTCAGCGATCCTTAATAGAGTGTCC
CCCTTGCTTCCGAGTGTCCTGAAGTTGCCAGTCAGATCTCTAACATACTTCAGCACACGAAAAGACAAGAGAAAGACTGT
GAAAGCTGTCATCTACAGGTTTCTTCGACTTCATTGTGGCCTTTGGGTGAGGAGAAAGGCTGGTTATAAGAAAAAATTAT
GGAAAAAGGAACCTGCAAGAAAAAAGGATTGAGGGAATTTGTATTCTGCAATAAAACCCAGAGTAAACTCTTAAGATAAA
GTGGCGACGTCCTTCTGGGAGAGGTGAAAC

Alignment

ORF - retro_pabe_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.95 %
• Parental protein coverage: 81.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRLPTSERNLTCG
          MAA.AFAGAVRAASGI..PLNILASS.Y.NCVKNASLISALSTGRFSHIQTPVVSSTPRL.TSERNLTCG
Retrocopy MAAFAFAGAVRAASGI*WPLNILASSAYQNCVKNASLISALSTGRFSHIQTPVVSSTPRLTTSERNLTCG

Parental  HTSVILNRVAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKTPAR
          HTS.ILNRV.P.LPSVLKLPVRSLTYFS.RK.KRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKK.PAR
Retrocopy HTSAILNRVSPLLPSVLKLPVRSLTYFSTRKDKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKEPAR

Parental  -KKRLREFVFCNKTQSKLL-DKMTTSFWKRRN
          .KK.LREFVFCNKTQSKLL.DK..TSFW.R.N
Retrocopy <KKGLREFVFCNKTQSKLL>DKVATSFWER*N

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	14.93 RPM
SRP007412_cerebellum	0.00 RPM	10.34 RPM
SRP007412_heart	0.00 RPM	12.34 RPM
SRP007412_kidney	0.00 RPM	11.57 RPM
SRP007412_liver	0.00 RPM	10.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_541 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_541 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_681
Pan troglodytes	retro_ptro_489

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019467	1 retrocopy	retro_cjac_203,
Dasypus novemcinctus	ENSDNOG00000008329	1 retrocopy	retro_dnov_404,
Macropus eugenii	ENSMEUG00000004773	1 retrocopy	retro_meug_1703,
Mus musculus	ENSMUSG00000052962	1 retrocopy	retro_mmus_1777,
Nomascus leucogenys	ENSNLEG00000002756	4 retrocopies	retro_nleu_1103, retro_nleu_1362, retro_nleu_2217, retro_nleu_781,
Otolemur garnettii	ENSOGAG00000004048	1 retrocopy	retro_ogar_2600,
Pongo abelii	ENSPPYG00000012214	5 retrocopies	retro_pabe_1817, retro_pabe_2837, retro_pabe_3724, retro_pabe_541 , retro_pabe_595,
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,