RetrogeneDB ID: retro_pabe_3471

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:48331146..48332083(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PES1
• Ensembl ID: ENSPPYG00000011716
• Aliases: None
• Description: pescadillo ribosomal biogenesis factor 1 [Source:HGNC Symbol;Acc:8848]

Sequence

>retro_pabe_3471
ATGTGCAGACCATTCACCGTGGAGTTCATGCACTACATCATCGCTGCTAGTGCCCTGCCACAAGGTCTTCCTGTCCATCA
AAGGCATTTACTACCAGGTCAAGGTCTCGGAACAGCCCATCATGTGAATCACCACTTATGCCTTCTCCCATGACCACCCA
ACAGACATGGACTACAGGGTCATGGCCACCTTCACCGAGTTCTACAGCACCCTGCTGGGCTTCGTCAACTTCCGCCTCTA
CCAGTGGCTCAACCTCCACTACCCACTGAAGCTTGAGGGTCAGGCCCAAGAAGAGGCAAAGGCCAGTGAGGGCACCCATG
CGTTGGACTCTGAGAGCTCCATGGAGAAAATGGCTGCCCTCAGTGCCAGCCTGGCCCTCATAGTGGTGCCTGCCACAGAG
GAGGAGCCCAAGGTGGATGAGTTTCCCACCAATGGGGAGATGTCAGCACAGGAGGAAGACTGCAGGAAGGAGCTGGAGGT
GCAGGAGAAGCACAAGAAGCTTTCTGAGGGCCTAAAGTTCTTCCTGAACTGAGAGGTGCCCCGTGAGGCCCTGGCCTTTG
TCATCAGTTTTTGGGGGGAAGTGTCCTGGGACAAGTCTTTGTGCATCGGGGCCACCTATGACATCACGGACTCCCGCATC
ACCCACCAGATTGTCGACTGGCCTGGGCAGCAGACCTCCATCATTGGCAGGAGCTATGTGCAGCCCCAGTGGGTGTTTGA
CTCGGTGAACGCTAGGCTTCTCCTCCCCGTGGCAGAGTACTTCCCTGGGGTGCAGCTGCCCCCACACCTTTCACCTTTTG
TGACTGAGAAGGAAGGAGATTACCTCCCACCTGAAAAACTGAGGCTGCTGGCTCTGCAGCAGGGAGAGGACCCAGGAATC
CTGAATGCATCAGAAGAGGAGGAGGAAGAGGACGACGACAACGAAAATGATGGTGAT

Alignment

ORF - retro_pabe_3471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 53.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LCRRLTVEFMHYIIAARAL-RKVFLSIKGVYYQAEVLGQPIVWITPYAFSHDHPTDVDYRVMATFTEFYT
          .CR..TVEFMHYIIAA.AL..KVFLSIKG.YYQ..V..QPI..IT.YAFSHDHPTD.DYRVMATFTEFY.
Retrocopy MCRPFTVEFMHYIIAASAL>HKVFLSIKGIYYQVKVSEQPIM*ITTYAFSHDHPTDMDYRVMATFTEFYS

Parental  TLLGFVNFRLYQLLNLHYPPKLEGQAQAEAKASEGIYALDSESSMEKLAALSASLARVVVPATEEEAEVD
          TLLGFVNFRLYQ.LNLHYP.KLEGQAQ.EAKASEG..ALDSESSMEK.AALSASLA..VVPATEEE..VD
Retrocopy TLLGFVNFRLYQWLNLHYPLKLEGQAQEEAKASEGTHALDSESSMEKMAALSASLALIVVPATEEEPKVD

Parental  EFPTDGEMSAQEEDRRKELEAQENHKKLFEGLKFFLNREVPREALAFIIRSFGGEVSWDKSLCIGATYDV
          EFPT.GEMSAQEED.RKELE.QE.HKKL.EGLKFFLN.EVPREALAF.I.SF.GEVSWDKSLCIGATYD.
Retrocopy EFPTNGEMSAQEEDCRKELEVQEKHKKLSEGLKFFLN*EVPREALAFVI-SFWGEVSWDKSLCIGATYDI

Parental  TDSRITHQIVDRPGQQTSVIGRCYVQPQWVFDSVNARLLLPVAEYFPGVQLPPHLSPFVTEKEGDYVPPE
          TDSRITHQIVD.PGQQTS.IGR.YVQPQWVFDSVNARLLLPVAEYFPGVQLPPHLSPFVTEKEGDY.PPE
Retrocopy TDSRITHQIVDWPGQQTSIIGRSYVQPQWVFDSVNARLLLPVAEYFPGVQLPPHLSPFVTEKEGDYLPPE

Parental  KLKLLALQRGEDPGNLNESEEEEEEDDDNESDGD
          KL.LLALQ.GEDPG.LN.SEEEEEEDDDNE.DGD
Retrocopy KLRLLALQQGEDPGILNASEEEEEEDDDNENDGD

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	43.57 RPM
SRP007412_cerebellum	0.00 RPM	36.12 RPM
SRP007412_heart	0.27 RPM	15.92 RPM
SRP007412_kidney	0.10 RPM	70.27 RPM
SRP007412_liver	0.06 RPM	43.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3471 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3471 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4133
Pan troglodytes	retro_ptro_2809

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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,