RetrogeneDB ID: retro_pabe_3285

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:114797431..114798271(+)
• Located in intron of: ENSPPYG00000018818

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRBF2
• Ensembl ID: ENSPPYG00000002411
• Aliases: None
• Description: Nuclear receptor-binding factor 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R4C9]

Sequence

>retro_pabe_3285
GAAGGACCCCTCAACCTGGCTCATCAGATGAGCAGACGTTTATTAGCTGCAGGCAAATACAAAGAGGCTATTTCTTGTCA
CAGAAAGGCTGCAGCGTATCTTTCTGAAGCCATGAAGCTGACACAGTCTGAGCAGGCTCATCTTTCACTGGAATTGCAAA
GAGATAGCCATATGAAACAGCTCCTCCTCATCCAAGAGAGATGGAAAAGGGCCCAGCGTGAAGAAAGATTGAAAGGCCAG
CAGAACACAGACAAGGATGTAGCTGCCCATCTTCAGGCATCTCACAAACCCTCTGCAAAGGATGCAGAGGGCCAGAGTCC
CCTTTCTCAGAAGTACAGCCCTTCCACAGAGAAACGCCTGCCTGAGATTCAGGGGATCTTTGACAGGGATCCAGACACAC
TACTATATTTACTTCAGCAAAAGAGTGAGCCAGCAGAGCCATGTATTGGAAGCAAAGCCCCAAAAGATGATAAAACAATT
ATAGAGGAGCAGGCAACCAAAATTGCAGATTTGAAGAGGCATGTGGAATTCCTTGTGGCAGAGAATGAAAGATTAAGGAA
AGAAAATAAACAACTAAAGGCTGAAAAGGCCAGACTTCTAAAAGGTCCAATAGAACAGGAGCTGGATGTAGGTGCTGATT
TTGTAGAAACATCAGAGTTATGGAGCTTGCCACCACATTCAGAAACTGCTACAGCCTCCTCAACCTGGCAGAAGTTCGCA
GAAAATAACAGGAAAGCCAAGGACATTCCTATCCCCAGTCTTTCTCCCTTGGATTTTGCATCTCCAGAACTTCCTCTTAC
GGAGCTCTCTGAAGATATTCTGAAAGGATTTATGAATAAT

Alignment

ORF - retro_pabe_3285 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 98.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQER
          EGPLNLAHQ.SR...RLLAAGKY.EAISCH.KAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQER
Retrocopy EGPLNLAHQMSR---RLLAAGKYKEAISCHRKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQER

Parental  WKRAQREERLKAQQNTDKDVAAHLQTSHKPSAEDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPDTLLYL
          WKRAQREERLK.QQNTDKDVAAHLQ.SHKPSA.DAEGQSPLSQKYSPSTEK.LPEIQGIFDRDPDTLLYL
Retrocopy WKRAQREERLKGQQNTDKDVAAHLQASHKPSAKDAEGQSPLSQKYSPSTEKRLPEIQGIFDRDPDTLLYL

Parental  LQQKSEPAEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGPIEKE
          LQQKSEPAEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGPIE.E
Retrocopy LQQKSEPAEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGPIEQE

Parental  LDVDADFVETSELWSLPPHSETATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDILKGF
          LDV.ADFVETSELWSLPPHSETATASSTWQKFA.N..KAKDIPIP.L.PLDF.SPELPL.ELSEDILKGF
Retrocopy LDVGADFVETSELWSLPPHSETATASSTWQKFAENNRKAKDIPIPSLSPLDFASPELPLTELSEDILKGF

Parental  MNN
          MNN
Retrocopy MNN

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	15.59 RPM
SRP007412_cerebellum	0.00 RPM	12.04 RPM
SRP007412_heart	0.00 RPM	4.61 RPM
SRP007412_kidney	0.00 RPM	9.88 RPM
SRP007412_liver	0.00 RPM	33.57 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3285 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3285 has 0 orthologous retrocopies within eutheria group .

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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,