RetrogeneDB ID: retro_ptro_2809

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:14229392..14230332(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PES1
• Ensembl ID: ENSPTRG00000014251
• Aliases: None
• Description: Pan troglodytes pescadillo ribosomal biogenesis factor 1 (PES1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246365]

Sequence

>retro_ptro_2809
ATGTGCAGACCATTCACCATGGAGTTCATGCACTACATCATTGCTGCTAGTGCCCTGCCACAAGGTCTTCCTGTCCATCA
AAGGCATTTACTACCAGGTCAAGGTCCTGGGACAGCCCATCATGTGAATCACCACTTATGCCTTCTCCCATGACCACCCA
ACAGACATGGACTACAGGGTCATGGCCACCTTCACCGAGTTCTACAGCACCCTGCTGGGCTTCATCAACTTCCACCTCTA
CCAGTGGCTCAACCTCCACTACCCACTGAAGCTCGAGGGTCAGGCCCAAGAAGAGGCAAAGGCCAGTGAGGGCACCCATG
CGTTGGACTCTGAGAGCTCCATGGAGAAAATGGCTGCCCTCACTGCCAGCCTGGCCCACGTGGTGGTGCCTGCCACAGAG
GAGGAGCCCGAGGTGGATGAGTTTCCTGCCAATGGGGAGATGTCAGCACAGGAGGAAGACCGCAGGAAGGAGCTGGAGGG
GCAGGAGAAGCACAAGAAGCTTTCTGAGGGCCTAAAGTTCTTCCTGAACCAAGGGGTGCCCTGTGAAGCCCTGGCCTTCG
TCATCAGTTTTTGGGGGGAAGTGTCCTGGGACAAGTCTTTGTGCATCAGGGCCACCTATGACATCACGGACTCCCGCATC
ACCCACCAGATTGTCGACTGGCCTGGGCAGCAGACCTCCATCATTGGCAGGTGCTACATGCAGCCCCAGTGGGTGATTGA
CTCGGTGAACGCTAGGCTTCTCCTCCTCATGGCAGAGTACTTCCCTGGGGTGCAGCTGCCCCCACACCTTTCACCTTTTG
TGACCAAGAAGGAAGGAGATTACATCCCACCTGAAAAACTGAGGCTGCGGGCTCTGCAGCAGGCAGAGGACCCAGGAATC
CTGAATGCATCAGAAGAAGAGGAGAAAGAGGACGACAACAATGAAAATGATGGTGATGAA

Alignment

ORF - retro_ptro_2809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 53.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LCRRLTVEFIHYIIAARAL-RKVFLSIKGIYYQAEVLGQPIVWITPYAFSHDHPTDVDYRVMATFTEFYT
          .CR..T.EF.HYIIAA.AL..KVFLSIKGIYYQ..VLGQPI..IT.YAFSHDHPTD.DYRVMATFTEFY.
Retrocopy MCRPFTMEFMHYIIAASAL>HKVFLSIKGIYYQVKVLGQPIM*ITTYAFSHDHPTDMDYRVMATFTEFYS

Parental  TLLGFVNFRLYQLLNLHYPPKLEGQAQAEAKASEGTYALDSESSMEKLAALSASLARVVVPATEEEAEVD
          TLLGF.NF.LYQ.LNLHYP.KLEGQAQ.EAKASEGT.ALDSESSMEK.AAL.ASLA.VVVPATEEE.EVD
Retrocopy TLLGFINFHLYQWLNLHYPLKLEGQAQEEAKASEGTHALDSESSMEKMAALTASLAHVVVPATEEEPEVD

Parental  EFPTDGEMSAQEEDRRKELEAQEKHKKLFEGLKFFLNREVPREALAFIIRSFGGEVSWDKSLCIGATYDV
          EFP..GEMSAQEEDRRKELE.QEKHKKL.EGLKFFLN..VP.EALAF.I.SF.GEVSWDKSLCI.ATYD.
Retrocopy EFPANGEMSAQEEDRRKELEGQEKHKKLSEGLKFFLNQGVPCEALAFVI-SFWGEVSWDKSLCIRATYDI

Parental  TDSRITHQIVDRPGQQTSVIGRCYVQPQWVFDSVNARLLLPVAEYFPGVQLPPHLSPFVTEKEGDYVPPE
          TDSRITHQIVD.PGQQTS.IGRCY.QPQWV.DSVNARLLL..AEYFPGVQLPPHLSPFVT.KEGDY.PPE
Retrocopy TDSRITHQIVDWPGQQTSIIGRCYMQPQWVIDSVNARLLLLMAEYFPGVQLPPHLSPFVTKKEGDYIPPE

Parental  KLKLLALQRGEDPGNLNESEEEEEEDDNNEGDGDE
          KL.L.ALQ..EDPG.LN.SEEEE.EDDNNE.DGDE
Retrocopy KLRLRALQQAEDPGILNASEEEEKEDDNNENDGDE

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	0.30 RPM	38.14 RPM
SRP007412_cerebellum	0.00 RPM	48.40 RPM
SRP007412_heart	0.03 RPM	12.94 RPM
SRP007412_kidney	0.00 RPM	43.67 RPM
SRP007412_liver	0.00 RPM	87.40 RPM
SRP007412_testis	0.11 RPM	72.61 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2809 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2809 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4133
Pongo abelii	retro_pabe_3471

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010617	1 retrocopy	retro_cjac_3182,
Cavia porcellus	ENSCPOG00000003565	1 retrocopy	retro_cpor_986,
Homo sapiens	ENSG00000100029	1 retrocopy	retro_hsap_4133,
Otolemur garnettii	ENSOGAG00000005804	1 retrocopy	retro_ogar_1719,
Pongo abelii	ENSPPYG00000011716	1 retrocopy	retro_pabe_3471,
Pan troglodytes	ENSPTRG00000014251	2 retrocopies	retro_ptro_2018, retro_ptro_2809 ,
Rattus norvegicus	ENSRNOG00000004515	2 retrocopies	retro_rnor_2953, retro_rnor_824,
Tupaia belangeri	ENSTBEG00000009825	1 retrocopy	retro_tbel_1000,