RetrogeneDB ID: retro_ptro_1780

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:46725899..46726757(+)
• Located in intron of: ENSPTRG00000030255

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_1780
ATGGAAGTAATGGAAGGACCCCTCAACCTGGCTCATCAGCAGAGCAGACGAGCCGACCGTTTATTAGCTGCAGGCAAATA
CGAAGAGGCGATTTCTTGTCACAAAAAGGCTGCGGCATATCTTTCTGAAGCCATGAAGCTGACACAATCTGAGCAGGCTC
ATCTTTCACTGGAATTGCAAAGGGATAGCCACATGAAACAGCTCCTCCTCATCCAAGAGAGATGGAAAAGGGCCCAGCGT
GAGGAAAGATTGAAAGCCTAGCAGAACACAGACAAGGATGTAGCTGCCCATCTTCAGGCATCTCACAAACTCTCTGCCGA
GGATGCGGAGGGCCAGAGCCCCCTTTCTCAGAAGTACAGCCCTTCTTCAGAGAAACGCCTGCCTGAGATTCAGGGGATCT
TTGACAGGGATCCAAACACACTACTATATTTACTTCAGCAAAAGAGTGAGCCAGCAGAGCCATGTATTGGAAGCAAAGCC
CCAGAAGATGATAAAACAATTATAGAGGAGTAGGCAACCAAAATTGCAGATTTGAAGAGGCATGTGGAATTCCTTGTGGC
TGAGAATGAAAGATTAAGGAAAGAAAATAACTAAAGGCTGAAAAGGCCAGACTTCTAAAAAGGTCCAGTAGAAAAAGAGC
TGGATGTAGATGCTGATTTTGTAGAAACGTCAGAATTACGGAGCTTGCCGCCACATTCAGAAACTGCTACAGCCTCCTCA
ACCTGGCAGAAGTTTGCAGCAAATGCCGGGAAAGCCAAGGACATTCCAATCCCCAGTCTTCCTCCCTTGGATTTTACATC
TCCAGAACTTCCCCTTATGGATCTCCCTGAGAATATTCTGAAAGGATTTATGAATAAT

Alignment

ORF - retro_ptro_1780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
          MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
Retrocopy MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL

Parental  IQERWKRAQREERLKAQQNTDKDAAAHLQTSHKPSAEDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPDT
          IQERWKRAQREERLKA.QNTDKD.AAHLQ.SHK.SAEDAEGQSPLSQKYSPS.EK.LPEIQGIFDRDP.T
Retrocopy IQERWKRAQREERLKA*QNTDKDVAAHLQASHKLSAEDAEGQSPLSQKYSPSSEKRLPEIQGIFDRDPNT

Parental  LLYLLQQKSEPAEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGP
          LLYLLQQKSEPAEPCIGSKAP.DDKTIIEE.ATKIADLKRHVEFLVAENERLRKEN...........KGP
Retrocopy LLYLLQQKSEPAEPCIGSKAPEDDKTIIEE*ATKIADLKRHVEFLVAENERLRKEN-N*RLKRPDF*KGP

Parental  IEKELDVDADFVETSELWSLPPHSETATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDI
          .EKELDVDADFVETSEL.SLPPHSETATASSTWQKFAAN.GKAKDIPIP.LPPLDF.SPELPLM.L.E.I
Retrocopy VEKELDVDADFVETSELRSLPPHSETATASSTWQKFAANAGKAKDIPIPSLPPLDFTSPELPLMDLPENI

Parental  LKGFMNN
          LKGFMNN
Retrocopy LKGFMNN

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	12.39 RPM
SRP007412_cerebellum	0.07 RPM	9.97 RPM
SRP007412_heart	0.00 RPM	3.21 RPM
SRP007412_kidney	0.03 RPM	10.41 RPM
SRP007412_liver	0.03 RPM	31.20 RPM
SRP007412_testis	0.53 RPM	13.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1780 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1780 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2643
Pongo abelii	retro_pabe_2327
Macaca mulatta	retro_mmul_1523

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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,