RetrogeneDB ID: retro_ptro_2715

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:106384136..106384995(+)
• Located in intron of: ENSPTRG00000020504

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRBF2
• Ensembl ID: ENSPTRG00000002539
• Aliases: None
• Description: None

Sequence

>retro_ptro_2715
ATGGAAGTAATGAAGGACCCCTCAACGTGGCTCATCAACAGAGCAGATGAGCAGACCGTTTATTAGCTGTAGGCAAATAC
GAAGAGGCTATTTCTTGTCACAAAAAGGCTGCAGCGTATCTTTCTGAAGCCATGAAGCTGACACAGTCTGAGCAGGCTCA
TCTTTCACTGGAATTGCAAAGGGATAGCCATATGAAACAGCTCCTCCTCATCCAAGAGAGATGGAAAAGGGCCCAGGGTG
AAGCAAGATTGAAAGCCCAGCAGAACACAGACAAGGATGTAGCTGCCCATCTTCAGGCATCTCACAAACCCTCTGTAGAG
GATGCAGAGGGCCAGAGTCCCCTTTCTCAGAAGTACAGCCCTTCCACAGAGAAATGTCTGCCTGAGATTCAGGGGATCTT
TGACAGGGATCCAGACACACTACTATATTTACTTCAGCAAAGGAGTGAGCCAGCAGAGCCATGTATTGGAAGTAAAGCCC
CAAAAGACGATAAAACAATTACAGAGGAGCAGGCAACCAAAATTGCAGATTTGAAGAGGCATGTGGAATTCCTTGTGGCA
GAGAATGAAAGATTAAGGGAAGAAAATAACAACTAAAGGCTGAAAAGGCCAGACTTCTAAAAGGTCCAATAGAAAAGGAG
CTGGATGTAGATGCTGATTTTGTAGAAACATCAGAGTTATGGAGCTTGCCACCACATTCAGAAACTGCTACAGCCTCCTC
AACCTGGCAGAAGTTTGCAGCAAATACTGGGAAAGCCAAGGACATTCCTGTCCCCAATCTTCCGCCCTTGGATTTTCCAT
CTACAGAACTTCCTCTTATGGAGCTCTCTGAGGATATTCTGAAAGGATTTATGAATAAT

Alignment

ORF - retro_ptro_2715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEVM-EGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLL
          MEVM.EGPLN.AHQQSR.ADRLLA.GKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLL
Retrocopy MEVM<EGPLNVAHQQSR*ADRLLAVGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLL

Parental  LIQERWKRAQREERLKAQQNTDKDAAAHLQTSHKPSAEDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPD
          LIQERWKRAQ.E.RLKAQQNTDKD.AAHLQ.SHKPS.EDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPD
Retrocopy LIQERWKRAQGEARLKAQQNTDKDVAAHLQASHKPSVEDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPD

Parental  TLLYLLQQKSEPAEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENK-QLKAEKARLLK
          TLLYLLQQ.SEPAEPCIGSKAPKDDKTI.EEQATKIADLKRHVEFLVAENERLR.EN..QLKAEKARLLK
Retrocopy TLLYLLQQRSEPAEPCIGSKAPKDDKTITEEQATKIADLKRHVEFLVAENERLREENN<QLKAEKARLLK

Parental  GPIEKELDVDADFVETSELWSLPPHSETATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSE
          GPIEKELDVDADFVETSELWSLPPHSETATASSTWQKFAANTGKAKDIP.PNLPPLDFPS.ELPLMELSE
Retrocopy GPIEKELDVDADFVETSELWSLPPHSETATASSTWQKFAANTGKAKDIPVPNLPPLDFPSTELPLMELSE

Parental  DILKGFMNN
          DILKGFMNN
Retrocopy DILKGFMNN

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	0.07 RPM	12.39 RPM
SRP007412_cerebellum	0.04 RPM	9.97 RPM
SRP007412_heart	0.00 RPM	3.21 RPM
SRP007412_kidney	0.00 RPM	10.41 RPM
SRP007412_liver	0.00 RPM	31.20 RPM
SRP007412_testis	0.00 RPM	13.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2715 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2715 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3999
Gorilla gorilla	retro_ggor_2685
Pongo abelii	retro_pabe_3286

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004648	3 retrocopies	retro_chof_1032, retro_chof_2250, retro_chof_2568,
Homo sapiens	ENSG00000148572	3 retrocopies	retro_hsap_2643, retro_hsap_3999, retro_hsap_433,
Gorilla gorilla	ENSGGOG00000013016	2 retrocopies	retro_ggor_1846, retro_ggor_2685,
Macropus eugenii	ENSMEUG00000010849	3 retrocopies	retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta	ENSMMUG00000017726	1 retrocopy	retro_mmul_1523,
Monodelphis domestica	ENSMODG00000017183	1 retrocopy	retro_mdom_1995,
Mus musculus	ENSMUSG00000075000	2 retrocopies	retro_mmus_1278, retro_mmus_1279,
Otolemur garnettii	ENSOGAG00000005856	1 retrocopy	retro_ogar_2110,
Pongo abelii	ENSPPYG00000002411	3 retrocopies	retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes	ENSPTRG00000002539	3 retrocopies	retro_ptro_1780, retro_ptro_194, retro_ptro_2715 ,
Rattus norvegicus	ENSRNOG00000000641	2 retrocopies	retro_rnor_1681, retro_rnor_994,
Sarcophilus harrisii	ENSSHAG00000004744	1 retrocopy	retro_shar_427,
Ictidomys tridecemlineatus	ENSSTOG00000011341	1 retrocopy	retro_itri_183,