RetrogeneDB ID: retro_hsap_1429

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:65066960..65068363(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000259010
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUP50
• Ensembl ID: ENSG00000093000
• Aliases: NUP50, NPAP60, NPAP60L
• Description: nucleoporin 50kDa [Source:HGNC Symbol;Acc:8065]

Sequence

>retro_hsap_1429
ATGGCCAAAAGAAATGCCGAGAAGGAACTGACAGATAGGAATTGGGATCAAGAAGATGAAGCTGAAGAGGTGGGAACATT
CTCCGTGGCCAGTGAGGAAGTCTTGAAGAATAGAGCCATAAAGAAAGCAAAGCGCAGAAATGGTGGATTCGAATCTGACA
GTAGAGGAGACTTTAAAGGTTTTAAAGGTTTGGTGGTACCTTTTGGAGGAGGACGGTTTCCTGGATTTGGTAGTGGCGCT
GGAGGGAAGCCTTTGGAAGGACTGTCGAATGGAAACAACATAACCAGTGCCCCTCCCTTCACCAGTGCAAAGGCAGTGGC
AGAGCCCAAGGTAGCCTTTGGTTCTCTTGCTGCAAATGGCCCTACCGCCTTGGTTGATAAAAATGTTTCAAATCCCAAAA
CTAATGGGGACAGTCAGCAGCCCTCCTCCTCTGGCCTTGCTTCCAGTAAAGCTTGTGTCGGAAATGCCTATCACAAGCAG
TTGGCCGCCTTGGACTGCTCCGTGCGGGATTGGATGGTGAAGCACGCGAATACAAACTCCCTCTGTGATCTGACACCTAT
CTTTAAAGACTATGAGAAATATTTAGCAAACATTGAACAGCAACAAGGGAACAATGGCAGGAATTCTGAAAGTGAATCTA
ACAAAGCGGCGGCTGAAACACAGTCTCCTTCCCTTTTTAGCTCAACAAAATTACAGCAAGAGTCAACGTTTTTGTTTCAT
GGCAGCAAAACTGAAGATACACCTGACAAGAAGGTGGAGGTGGCATCTGAAAAGAAAACGGACCCATCATCACTAGGAGC
GACAAGTGCCTCATTTAATTTCGGCGAGAAAGTTGATAGCTCTGTTTTGGGCTCATTAAGCTCTGTCCCCCGACTGGATT
TTCATTCTCCCCTGGAAACTCTAGTTTATTTGGCAAAGATATTATCCAGAGTAAACCAGTCTCTTCACCATTTCCCACTA
AACCATTGGAGGGCCAAGCGGAAGGTGACAGTGGTGAATGCAAAGGTGGAGATTAAGAAGAGAATGATGAGCCACCCAAA
GTAGTAGTTACCGAAGTAAAAGAAGATGCTTTTTACTCCAAAAAGTGTAAACTATTTTACAAGAAAGACAATGAGTTTAA
AGAGAAAGGCATAGGTACTCTGCATTTAAAACCTACGGCAAATCAGAAGACATAGCTTTTGGTGCGGGCAGACACCAATT
TAGGCAACATATTGCTGAATGTTCTGATTCCACCCAATATGCCATGTACGCGAACAGGGAAAAATAACGTTCTTATCGTC
TGTGTTCCAAATCCACCAATCGACGAGAAGAATGCCACCATGCCAGTCACCATGTTGATTCGGGTAAAAACCAGCGAGGA
TGCAGACGAGTTGCACAAAATTTTACTGGAGAAAAAGGATGCC

Alignment

ORF - retro_hsap_1429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKRNAEKELTDRNWDQEDEAEEVGTFSMASEEVLKNRAIKKAKRRNVGFESDTGGAFKGFKGLVVPSGG
          MAKRNAEKELTDRNWDQEDEAEEVGTFS.ASEEVLKNRAIKKAKRRN.GFESD..G........VVP.GG
Retrocopy MAKRNAEKELTDRNWDQEDEAEEVGTFSVASEEVLKNRAIKKAKRRNGGFESDSRGDXXXXXXXVVPFGG

Parental  GRFSGFGSGAGGKPLEGLSNGNNITSAPPFASAKAAADPKVAFGSLAANGPTTLVDK-VSNPKTNGDSQQ
          GRF.GFGSGAGGKPLEGLSNGNNITSAPPF.SAKA.A.PKVAFGSLAANGPT.LVDK.VSNPKTNGDSQQ
Retrocopy GRFPGFGSGAGGKPLEGLSNGNNITSAPPFTSAKAVAEPKVAFGSLAANGPTALVDKNVSNPKTNGDSQQ

Parental  PSSSGLASSKACVGNAYHKQLAALNCSVRDWIVKHVNTNPLCDLTPIFKDYEKYLANIEQQHGNSGRNSE
          PSSSGLASSKACVGNAYHKQLAAL.CSVRDW.VKH.NTN.LCDLTPIFKDYEKYLANIEQQ.GN.GRNSE
Retrocopy PSSSGLASSKACVGNAYHKQLAALDCSVRDWMVKHANTNSLCDLTPIFKDYEKYLANIEQQQGNNGRNSE

Parental  SESNKVAAETQSPSLFGSTKLQQESTFLFHGNKTEDTPDKKMEVASEKKTDPSSLGATSASFNFGKKVDS
          SESNK.AAETQSPSLF.STKLQQESTFLFHG.KTEDTPDKK.EVASEKKTDPSSLGATSASFNFG.KVDS
Retrocopy SESNKAAAETQSPSLFSSTKLQQESTFLFHGSKTEDTPDKKVEVASEKKTDPSSLGATSASFNFGEKVDS

Parental  SVLGSLSSVPL-TGFSFSPGNSSLFGKDTTQSKPVSSPFPTKPLEGQAEGDSGECKGGDEEENDEPPKVV
          SVLGSLSSVP..TGFSFSPGNSSLFGKD..QSKPVSSPFPTKPLEGQAEGDSGECKGGD.EENDEPPKVV
Retrocopy SVLGSLSSVPR<TGFSFSPGNSSLFGKDIIQSKPVSSPFPTKPLEGQAEGDSGECKGGD*EENDEPPKVV

Parental  VTEVKEEDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQLLVRADTNLGNILLNVLIPPNMPCTR
          VTEVK.EDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKT.LLVRADTNLGNILLNVLIPPNMPCTR
Retrocopy VTEVK-EDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKT*LLVRADTNLGNILLNVLIPPNMPCTR

Parental  TGKNNVLIVCVPNPPIDEKNATMPVTMLIRVKTSEDADELHKILLEKKDA
          TGKNNVLIVCVPNPPIDEKNATMPVTMLIRVKTSEDADELHKILLEKKDA
Retrocopy TGKNNVLIVCVPNPPIDEKNATMPVTMLIRVKTSEDADELHKILLEKKDA

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
bodymap2_adipose	0.00 RPM	83.75 RPM
bodymap2_adrenal	0.00 RPM	77.48 RPM
bodymap2_brain	0.05 RPM	46.93 RPM
bodymap2_breast	0.00 RPM	45.62 RPM
bodymap2_colon	0.00 RPM	42.13 RPM
bodymap2_heart	0.00 RPM	19.20 RPM
bodymap2_kidney	0.00 RPM	57.37 RPM
bodymap2_liver	0.00 RPM	42.42 RPM
bodymap2_lung	0.00 RPM	52.48 RPM
bodymap2_lymph_node	0.04 RPM	72.22 RPM
bodymap2_ovary	0.10 RPM	66.51 RPM
bodymap2_prostate	0.00 RPM	42.47 RPM
bodymap2_skeletal_muscle	0.00 RPM	22.03 RPM
bodymap2_testis	0.21 RPM	78.41 RPM
bodymap2_thyroid	0.00 RPM	50.60 RPM
bodymap2_white_blood_cells	0.00 RPM	199.18 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1429 was not detected

EST

No EST(s) were mapped for retro_hsap_1429 retrocopy.

TSS

No TSS is located nearby retro_hsap_1429 retrocopy 5' end.

Lab

retro_hsap_1429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1429 has 0 orthologous retrocopies within eutheria group .

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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,