RetrogeneDB ID: retro_hsap_551

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:24446763..24447674(+)
• Located in intron of: ENSG00000120549

Retrocopy information

• Ensembl ID: ENSG00000223928
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUP35
• Ensembl ID: ENSG00000163002
• Aliases: NUP35, MP-44, MP44, NP44, NUP53
• Description: nucleoporin 35kDa [Source:HGNC Symbol;Acc:29797]

Sequence

>retro_hsap_551
ATGGCAGCCTTTGCCATGGAACTCCAGGTGCCTGCATTAGGATCTGAACCAATGATGCTGGCTTCATCTCCAAAGCCAGG
AGTTAATGCCCAGTTCTTACCTGGATTTTGAATGTGGAATTTGCCAGCCCTGGTGACTCCACAATCTCGATCAATTAGTG
GCCCTTCAGTAGGAGTAGTGGAAATGAGATCACCTTTACTTGCAGGTGGGTCACCACCACAACCAGTTTTACTAGCTCAT
AAAGATAAAAGTGGCGCTCCACAAGTTAGAAGTATATATGATGACATTTCTAGCCTGGGATTTGGATCAACACCTTTAAC
TTCAAGAAGACAGCCAAACATTTCATGATGCAGAGTCCTCTTACTGGAGTTACATCTACTCCTGGAACAGGGCAAAGTAC
GTTTAGTCCAGCAAATGTCGGTCAGTCATGAAAGATGACATTTTCTCCTTCCCGGTTGGATCCTTTTTATACTCAAGGAG
ATTCTTTGACTTCAGAAGGTCACCTTGATGACACTTGGGTGACTGTGTTCGGGTTTTCTCAAGCCTCTGCTTCCTACATA
TTATTACAATTTGCACAGTATGGGAATATCTTAAAACACATGATGTCTAACACAGGAAATTGAATGTATATTCATTATCA
GTCTAAACTGCAGGCTCGGAAAGCCTTAACCAAAGATGGGAGGATTTTTAGAGAATTCATCATGATTGGTGTAAAATCCT
GTATTGACTAAACTGTAATGGGAAGCACTGACAGACGTGCTTTATCATCTCCATCTTTCGCCTTTACACCACCAATCAAA
ACTTTAGGTACACTAGCACAACCTGAAAGTACTCCTAGGATTTCTGCCATGAGACCTCTTGCTACAGCATACAAAGATTC
TACTAGTGATTATCAGGTTATTTCTGACAGA

Alignment

ORF - retro_hsap_551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.39 %
• Parental protein coverage: 93.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAFAVEPQGPALGSEPMMLGSPTSPKPGVNAQFLPGFLMGDLPAPVTPQPRSISGPSVGVMEMRSPLLA
          MAAFA.E.Q.PALGSEPMML.S..SPKPGVNAQFLPGF.M..LPA.VTPQ.RSISGPSVGV.EMRSPLLA
Retrocopy MAAFAMELQVPALGSEPMMLAS--SPKPGVNAQFLPGF*MWNLPALVTPQSRSISGPSVGVVEMRSPLLA

Parental  GGSPPQPVVPAHKDKSGAPPVRSIYDDISSPGLGSTPLTSRRQPNIS-VMQSPLVGVTSTPGTGQSMFSP
          GGSPPQPV..AHKDKSGAP.VRSIYDDISS.G.GSTPLTSRRQPNIS..MQSPL.GVTSTPGTGQS.FSP
Retrocopy GGSPPQPVLLAHKDKSGAPQVRSIYDDISSLGFGSTPLTSRRQPNIS<MMQSPLTGVTSTPGTGQSTFSP

Parental  ASIGQPRKTTLSPAQLDPFYTQGDSLTSEDHLDDSWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGN
          A..GQ..K.T.SP..LDPFYTQGDSLTSE.HLDD.WVTVFGF.QASASYILLQFAQYGNILKH.MSNTGN
Retrocopy ANVGQS*KMTFSPSRLDPFYTQGDSLTSEGHLDDTWVTVFGFSQASASYILLQFAQYGNILKHMMSNTGN

Parental  WMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKSVMESSDRCALSSPSLAFTPPIKTLGTPTQPGS
          .M.I.YQSKLQARKAL.KDGRIF.E.IMIGVK.CID..VM.S.DR.ALSSPS.AFTPPIKTLGT..QP.S
Retrocopy *MYIHYQSKLQARKALTKDGRIFREFIMIGVKSCID*TVMGSTDRRALSSPSFAFTPPIKTLGTLAQPES

Parental  TPRISTMRPLATAYKASTSDYQVISDR
          TPRIS.MRPLATAYK.STSDYQVISDR
Retrocopy TPRISAMRPLATAYKDSTSDYQVISDR

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	0.24 RPM	7.20 RPM
bodymap2_adrenal	0.00 RPM	12.53 RPM
bodymap2_brain	0.00 RPM	3.68 RPM
bodymap2_breast	0.10 RPM	7.04 RPM
bodymap2_colon	0.00 RPM	9.09 RPM
bodymap2_heart	0.09 RPM	5.58 RPM
bodymap2_kidney	0.00 RPM	11.91 RPM
bodymap2_liver	0.00 RPM	11.24 RPM
bodymap2_lung	0.00 RPM	3.22 RPM
bodymap2_lymph_node	0.00 RPM	9.59 RPM
bodymap2_ovary	0.00 RPM	14.11 RPM
bodymap2_prostate	0.00 RPM	13.70 RPM
bodymap2_skeletal_muscle	0.00 RPM	4.93 RPM
bodymap2_testis	0.00 RPM	27.34 RPM
bodymap2_thyroid	0.00 RPM	9.91 RPM
bodymap2_white_blood_cells	0.00 RPM	5.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_551 was not detected

EST

No EST(s) were mapped for retro_hsap_551 retrocopy.

TSS

No TSS is located nearby retro_hsap_551 retrocopy 5' end.

Lab

retro_hsap_551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_551 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_414
Pongo abelii	retro_pabe_508
Macaca mulatta	retro_mmul_2387

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008469	1 retrocopy	retro_eeur_666,
Homo sapiens	ENSG00000163002	1 retrocopy	retro_hsap_551 ,
Gorilla gorilla	ENSGGOG00000009919	1 retrocopy	retro_ggor_500,
Macaca mulatta	ENSMMUG00000004140	1 retrocopy	retro_mmul_2387,
Nomascus leucogenys	ENSNLEG00000006423	1 retrocopy	retro_nleu_2019,
Pongo abelii	ENSPPYG00000012998	1 retrocopy	retro_pabe_508,
Pan troglodytes	ENSPTRG00000012711	1 retrocopy	retro_ptro_414,
Ictidomys tridecemlineatus	ENSSTOG00000000711	2 retrocopies	retro_itri_755, retro_itri_760,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).