RetrogeneDB ID: retro_ptro_850

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:18827742..18828488(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL3
• Ensembl ID: ENSPTRG00000015396
• Aliases: None
• Description: None

Sequence

>retro_ptro_850
TTGGCCTTGAAGCTGGGGATGATGCCTTTATGGACCAAGGATGGTCAAAAGCATGTGGTCACATTACTTCAGGTACAAGA
CTGTCATGTCCTAAAATATACTTCAAAGGAAAGCCGTAATGGAAAAACGGCAGCCCTGTCTGTAGGAGGCAAACTGTATC
ACGTTTTCATAAAGCTACACCTGTATTGGAATTTTACCGAGAACTTGGATTGCCGTCAAAACAGACAATTATAATCTTTA
ATGTAACAGATAATGCTGCAATTAAACCAGGCACTCTTCTTTATGCTGCTCACTTTTGTCCAGGACAGTATGTGGATGTC
ACAGCCAAAACTATTGGTAAAGGTTTTCAAGGTGTCATGAAAAGATGGGGATTTAAAGGCCAGCCTGCTACACATGGTCA
AACGAAAACCCACAGGAGACCTGGAGATATTTCAACTGGTGACATTGGCAGAGTCTGGCCTGGAACTAAAATGCCTGGAA
AAATGGGAAACATATATAGAACAGTATATGGACTGAAAATGTGGAGAATAAACACAAAGCACAACATAATCTATGTAAAC
GGCTCTGTACCTGGACATAAAAATTGCTTAGTAAGGGTCAGAGATTCTAAACTGCCTGCATATAAGGATCTCGGTAAAAA
TCTACCATTCCCTACGTATTTTCCTGATGGAGATGAAGAGGAACTACCGGAAGATTTGTATGATGAAAACGTGTGTCAGC
CTAGTGTGCCTTCTATTATGTTTGCC

Alignment

ORF - retro_ptro_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.4 %
• Parental protein coverage: 71.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IALKLGMMPLWTKDGQKHVVTLLQVQDCHVLKYTSKENCNGKMATLSVGGK-TVSRFRKATSILEFYREL
          .ALKLGMMPLWTKDGQKHVVTLLQVQDCHVLKYTSKE..NGK.A.LSVGGK.TVSRF.KAT..LEFYREL
Retrocopy LALKLGMMPLWTKDGQKHVVTLLQVQDCHVLKYTSKESRNGKTAALSVGGK<TVSRFHKATPVLEFYREL

Parental  GLPPKQTVKIFNITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHR
          GLP.KQT..IFN.TDNAAIKPGT.LYAAHF.PGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHR
Retrocopy GLPSKQTIIIFNVTDNAAIKPGTLLYAAHFCPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHR

Parental  RPGAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVRDSKLPAYK
          RPG...TGDIGRVWPGTKMPGKMGNIYRT.YGLK.WRINTKHNIIYVNGSVPGHKNCLV.VRDSKLPAYK
Retrocopy RPGDISTGDIGRVWPGTKMPGKMGNIYRTVYGLKMWRINTKHNIIYVNGSVPGHKNCLVRVRDSKLPAYK

Parental  DLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA
          DLGKNLPFPTYFPDGDEEELPEDLYDENVCQP..PSI.FA
Retrocopy DLGKNLPFPTYFPDGDEEELPEDLYDENVCQPSVPSIMFA

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	0.05 RPM	18.59 RPM
SRP007412_cerebellum	0.00 RPM	15.74 RPM
SRP007412_heart	0.03 RPM	16.64 RPM
SRP007412_kidney	0.03 RPM	40.33 RPM
SRP007412_liver	0.03 RPM	25.07 RPM
SRP007412_testis	0.00 RPM	45.10 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_850 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_850 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1236
Gorilla gorilla	retro_ggor_969

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021216	1 retrocopy	retro_cpor_324,
Dasypus novemcinctus	ENSDNOG00000014498	1 retrocopy	retro_dnov_178,
Homo sapiens	ENSG00000114686	1 retrocopy	retro_hsap_1236,
Gorilla gorilla	ENSGGOG00000011128	1 retrocopy	retro_ggor_969,
Microcebus murinus	ENSMICG00000009524	1 retrocopy	retro_mmur_1106,
Ochotona princeps	ENSOPRG00000000501	1 retrocopy	retro_opri_589,
Pan troglodytes	ENSPTRG00000015396	1 retrocopy	retro_ptro_850 ,
Sus scrofa	ENSSSCG00000011179	1 retrocopy	retro_sscr_126,