RetrogeneDB ID: retro_pabe_2723

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:21161130..21162516(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP50
• Ensembl ID: ENSPPYG00000011928
• Aliases: None
• Description: nucleoporin 50kDa [Source:HGNC Symbol;Acc:8065]

Sequence

>retro_pabe_2723
ATGGCCGAAAGAAATGCGGAGAAGGAACTGACAGGTAAGAATTGGGATCAAGAAGATGAAGCTGAAGAGGTGGGCACATT
GTCCGTGGCCAGTGAGGAAGTCTTGAAGAATAGAGCCATAAAGAAAGCAAAGCGCAGAAATGTTGGATTCGAATCTGACA
GTGGAGGAGCCTTTAAAGGTTTTAAAGGTTTTGTGGTACCTTCTGGAGGAGGACGGTTTCCTGGATTTGGTAGTGGTGCT
GGAGGGAAGCCTTTGGAAGGACTGTGGAATGGAAACAACATAACCAGTGCCCCTCCCTTCACCAGTGCAAAGGCAGTGGC
AGAGCCCAAGGTAGCCTTTGGTTCTCTTGCTGCAAATGGCCCTACCGCCTTGGTGGATAAAAAAGTTTCAAATCCCAAAA
CTAATGGGGACAGTCAGCAGCCCTCCTCCTCTGGCCTTGCTTCCAGTAAAGCTTGTGTCGGAAATGCCTGTCACAAGCAG
TTGGCCGCCTTGAACTGCTCTGTGCGGGATCGGATAGTGAAGCACGTGAATACAAATCCCCTCTGTGATCTGACACCTAT
CTTTAAAGACTATGAGAAATACTTAGCAAACATTGAACAGCAACAGGGGAACAGTGGCAGGAATTCTGAAAGTGAATCTA
ACAAAGCTGCGGCTGAAACACAGTCTCCTTCCCTTTTTGGTTCAACAAAATTACAGCAAGAGTCAGCGTTTTTGTTTCAT
GGCAACAAAACTGAAGATACACCTGACAAGAAGGTGGAGGTGGCATCTGAAAAGAAAACGGACCCATCATCACTAGGAGC
GACAAGTGCTCCATTTAATTTCAGCAAGAAAGTTGATAGCTCTGTTTTGGGCTCATTAAGCTCTGTCCCCCTGACTGGAT
TTTCATTCTCCCCTGGAAACTCCAGTTTATTTGGCAAAGATATTACCCAGAGTAAACCAGTCTCTTCACCATTTCCCACT
AAACCATTGGAGGGCCAAGCGGAAGGTGACAGTGGTGAATGCAAAGGTGGAGATGAAGAAGAGAATGATGAGCCACCCAA
AGTAGTAGTTACCGAAGTAAAAGAAGATGCTTTTTACTCCAAAAAGTGTAAACTATTTTACAAGAAAGATAATGAGTTTA
AAGAGAAAGGCATAGGTACTCTGCATTTAAAACCTACAGCAAATCAGAAGACACAGGCTTTGGTGCGGGCAGACACTAAT
TTAGGCAACATATTGCTGAATGTTCTGATTCCACCCAATATGCCATGTACGCGAACAGGGAAAAATAACGATCTTATTGT
CTGTGTTCCAAATCCACCAATTGACGAGAAGAATGCCACCATGCCGATTCGGGTAAAAACCAGCGAGGATGCAGACGAGT
TGCACAAAATTTTACTGGAGAAAAGG

Alignment

ORF - retro_pabe_2723 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKRNAEKELTDRNWDQEDEAEEVGTFSLASEEVLKNRAIKKAKRRNVGFESDSGGAFKGFKGLVVPSGG
          MA.RNAEKELT..NWDQEDEAEEVGT.S.ASEEVLKNRAIKKAKRRNVGFESDSGGA.......VVPSGG
Retrocopy MAERNAEKELTGKNWDQEDEAEEVGTLSVASEEVLKNRAIKKAKRRNVGFESDSGGAXXXXXXXVVPSGG

Parental  GRFPGFGSGAGGKPLEGLSNGNNITSAPPFTSAKAAAEPKVAFGSLPANGPTALVDK-VSNPKTNGDSQQ
          GRFPGFGSGAGGKPLEGL.NGNNITSAPPFTSAKA.AEPKVAFGSL.ANGPTALVDK.VSNPKTNGDSQQ
Retrocopy GRFPGFGSGAGGKPLEGLWNGNNITSAPPFTSAKAVAEPKVAFGSLAANGPTALVDKKVSNPKTNGDSQQ

Parental  PSSSGLASSKACVGSAYHKQLAALNCSVRDWIVKHVNTNPLCDLTPIFKDYEKYLANIEQQHGNSGRNSE
          PSSSGLASSKACVG.A.HKQLAALNCSVRD.IVKHVNTNPLCDLTPIFKDYEKYLANIEQQ.GNSGRNSE
Retrocopy PSSSGLASSKACVGNACHKQLAALNCSVRDRIVKHVNTNPLCDLTPIFKDYEKYLANIEQQQGNSGRNSE

Parental  SEPNKVAAETQSPSLFGSTKLQQESTFLFHGNKTEDTPDKKVEVASEKKTDPSSLGATSASFNFGKKVDS
          SE.NK.AAETQSPSLFGSTKLQQES.FLFHGNKTEDTPDKKVEVASEKKTDPSSLGATSA.FNF.KKVDS
Retrocopy SESNKAAAETQSPSLFGSTKLQQESAFLFHGNKTEDTPDKKVEVASEKKTDPSSLGATSAPFNFSKKVDS

Parental  SVLGSLSSVPLTGFSFSPGNSSVFGKDITQSKPVSSPFPTKPLEGQAEGYSGECKGGDEEENEEPPKVVV
          SVLGSLSSVPLTGFSFSPGNSS.FGKDITQSKPVSSPFPTKPLEGQAEG.SGECKGGDEEEN.EPPKVVV
Retrocopy SVLGSLSSVPLTGFSFSPGNSSLFGKDITQSKPVSSPFPTKPLEGQAEGDSGECKGGDEEENDEPPKVVV

Parental  TEVKEEDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQLLVRADTNLGNILLNVLIPPNMPCTRT
          TEVK.EDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQ.LVRADTNLGNILLNVLIPPNMPCTRT
Retrocopy TEVK-EDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQALVRADTNLGNILLNVLIPPNMPCTRT

Parental  GKNNVLIVCVPNPPIDEKNATMPVTMLIRVKTSEDADELHKILLEKK
          GKNN.LIVCVPNPPIDEKNATMP.....RVKTSEDADELHKILLEK.
Retrocopy GKNNDLIVCVPNPPIDEKNATMPI----RVKTSEDADELHKILLEKR

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	0.06 RPM	38.76 RPM
SRP007412_cerebellum	0.24 RPM	36.12 RPM
SRP007412_heart	0.00 RPM	8.43 RPM
SRP007412_kidney	0.00 RPM	21.38 RPM
SRP007412_liver	0.00 RPM	19.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2723 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2723 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3301

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016242	1 retrocopy	retro_cjac_4080,
Homo sapiens	ENSG00000093000	3 retrocopies	retro_hsap_1429, retro_hsap_3301, retro_hsap_3434,
Microcebus murinus	ENSMICG00000006840	1 retrocopy	retro_mmur_534,
Mus musculus	ENSMUSG00000016619	1 retrocopy	retro_mmus_1905,
Nomascus leucogenys	ENSNLEG00000013154	2 retrocopies	retro_nleu_1359, retro_nleu_1844,
Otolemur garnettii	ENSOGAG00000002320	1 retrocopy	retro_ogar_942,
Pongo abelii	ENSPPYG00000011928	1 retrocopy	retro_pabe_2723 ,