RetrogeneDB ID: retro_hsap_1724

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:18364813..18366373(+)
• Located in intron of: ENSG00000265785

Retrocopy information

• Ensembl ID: ENSG00000230662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TNPO1
• Ensembl ID: ENSG00000083312
• Aliases: TNPO1, IPO2, KPNB2, MIP, MIP1, TRN
• Description: transportin 1 [Source:HGNC Symbol;Acc:6401]

Sequence

>retro_hsap_1724
TCTGACTGGAATCTAAGGAAATGATCTGTTGCTGCCCTAGATGTTCTTGCAAACGTGCATCATGATGAACTGCTGCCATA
TATATTGCCCCTTTTGAAAGAATTACTTTTTCATCATGAATGGGTTGTTAAAGAATTAGCCATCTTGGGTTTAGGAACAG
TTGCTGAAGGTTTGCATGCAGGGCATGATTCCTTGCTTGCCTGAGCTTATTCCTCACCTTATTCAGTGCTTCTCTGATAA
AAAGGCTCTTGTCCGTTCCATAACATGCTGGACTCTTAGCCGCTATGCACACTGGGTAGTCAGCCAGCCACCAGACACGT
ACCTGAAGTCATTAATGACAGAGTTGCTAAAAGGCATCCTGGATAGCAACAAGAGAGTACCAGAAGCTGCCTGCAGTGCC
TTTGCTACCCTAGAAGAGGAGGCTTGTACAGAACTTGTTGCTTACCTTGCTTATATACTTGATACCCTGGTCTTTGCATT
TAGTAAATACCAGCATAAGAACCTGCTCATTCTTTACAATGCCAGAGGGACATTAGCAGATTCAGTAGGACATCATTTAA
ACAAACCAGAATATATTCAAATGCTAATGCCTCTACTGATCCAGAAACGGAACATGTTAAAGGATGAAGATAAAGATCTT
TTCCCTTTACCTGAGTGTCCATTTTCAGTTGCCACGGTGCTGCAGTCTGGCTTCCTTCCATACTGTGAACCTATGTATCA
GCATTGGGTAAACCTAGTACAGAAGACTCTTGCACAAGCCATACTAAGCAATGCTCAACCAGATCAATATGAAGCTCCAG
ATAAAGATTTTATGATAGTGGCTCTTGATTTACTGAGTGGCCTGGCTGAAGGACTTGGAGGCAATATTGAACAACTGGTA
GCCCGAAGTAACATCCTAACACTAACATATCAGTGCATGCAGGATAAAATGCCGGAAGTTCGACAGAGTTCTTTTGCCCT
GTTAAGTGACCTCACAAAAGCTTGCTTTCAGCATGTTAAGCCTTGTGTAGCTGATTTCATGCCAATATTGGGAACCAACC
TAACTCCAGAATTCATTTCAGTCTGCAACAATGACACATGAGCAATTGGAGAAATCTCCATTCAAATGGGTATAGAGATG
CAGCCTTATATCCCTATGGTGTTGCACCAGCTTGTAGAAATCATTAACAGACCCAACACACCAAAGACGTTGCTAAAGAA
TACAGCAGTAACAATTGGTTGTCTTGGTTATGTTTGTCCTCAAGAGGTGGTCCCCATGCTACAGCAGTTTACGAGACTCT
GGTGCACCTCTCTGAGAAACATAAGAGACAATGAGAAAAGGATTCAGCATTCCGTGGAATCTGCATCATGATCAGTGTGA
ATCCCCATGGCATAATCCAAGATTTTATATTTTTTTGTGATGCTGTTGCATCATGGATTAACCCAAAAGATTATCTCAGA
GACATGTTCTGTAAGATCCTTCATGGATTTAAAAATCAAATTGGCAATGAAAATGGGAGGCATTTCTCTGACCAGTTTCC
TCTTCCCTTAAAAGAGCATCTTGTAGCTTTTTATGGTGTT

Alignment

ORF - retro_hsap_1724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.85 %
• Parental protein coverage: 58.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SDWNLRKCSAAALDVLANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAIAEG-CMQGMIPYLPEL
          SDWNLRK.S.AALDVLANV..DELLP.ILPLLKELLFHHEWVVKE..IL.LG..AEG.CMQGMIP.LPEL
Retrocopy SDWNLRK*SVAALDVLANVHHDELLPYILPLLKELLFHHEWVVKELAILGLGTVAEG>CMQGMIPCLPEL

Parental  IPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKPLMTELLKRILDSNKRVQEAACSAFATLEE
          IPHLIQC.SDKKALVRSITCWTLSRYAHWVVSQPPDTYLK.LMTELLK.ILDSNKRV.EAACSAFATLEE
Retrocopy IPHLIQCFSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKSLMTELLKGILDSNKRVPEAACSAFATLEE

Parental  EACTELVPYLAYILDTLVFAFSKYQHKNLLILYDAIGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDE
          EACTELV.YLAYILDTLVFAFSKYQHKNLLILY.A.GTLADSVGHHLNKPEYIQMLMP.LIQK.NMLKDE
Retrocopy EACTELVAYLAYILDTLVFAFSKYQHKNLLILYNARGTLADSVGHHLNKPEYIQMLMPLLIQKRNMLKDE

Parental  DKDLFPLLECLSSVATALQSGFLPYCEPVYQRCVNLVQKTLAQAMLNNAQPDQYEAPDKDFMIVALDLLS
          DKDLFPL.EC..SVAT.LQSGFLPYCEP.YQ..VNLVQKTLAQA.L.NAQPDQYEAPDKDFMIVALDLLS
Retrocopy DKDLFPLPECPFSVATVLQSGFLPYCEPMYQHWVNLVQKTLAQAILSNAQPDQYEAPDKDFMIVALDLLS

Parental  GLAEGLGGNIEQLVARSNILTLMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLNP
          GLAEGLGGNIEQLVARSNILTL.YQCMQDKMPEVRQSSFALL.DLTKACFQHVKPC.ADFMPILGTNL.P
Retrocopy GLAEGLGGNIEQLVARSNILTLTYQCMQDKMPEVRQSSFALLSDLTKACFQHVKPCVADFMPILGTNLTP

Parental  EFISVCNNATWAIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLENTAITIGRLGYVCPQEVAPM
          EFISVCNN.T.AIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLL.NTA.TIG.LGYVCPQEV.PM
Retrocopy EFISVCNNDT*AIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLKNTAVTIGCLGYVCPQEVVPM

Parental  LQQFIRPWCTSLRNIRDNE-EKDSAFRGICTMISVNPSGVIQDFIFFCDAVASWINPKDDLRDMFCKILH
          LQQF.R.WCTSLRNIRDNE.EKDSAFRGIC.MISVNP.G.IQDFIFFCDAVASWINPKD.LRDMFCKILH
Retrocopy LQQFTRLWCTSLRNIRDNE<EKDSAFRGICIMISVNPHGIIQDFIFFCDAVASWINPKDYLRDMFCKILH

Parental  GFKNQVGDENWRRFSDQFPLPLKERLAAFYGV
          GFKNQ.G.EN.R.FSDQFPLPLKE.L.AFYGV
Retrocopy GFKNQIGNENGRHFSDQFPLPLKEHLVAFYGV

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	148.51 RPM
bodymap2_adrenal	0.00 RPM	114.10 RPM
bodymap2_brain	0.00 RPM	107.10 RPM
bodymap2_breast	0.00 RPM	164.83 RPM
bodymap2_colon	0.00 RPM	153.87 RPM
bodymap2_heart	0.00 RPM	113.37 RPM
bodymap2_kidney	0.00 RPM	162.96 RPM
bodymap2_liver	0.00 RPM	54.77 RPM
bodymap2_lung	0.00 RPM	141.72 RPM
bodymap2_lymph_node	0.00 RPM	144.18 RPM
bodymap2_ovary	0.00 RPM	158.88 RPM
bodymap2_prostate	0.00 RPM	181.25 RPM
bodymap2_skeletal_muscle	0.00 RPM	92.74 RPM
bodymap2_testis	0.00 RPM	211.25 RPM
bodymap2_thyroid	0.00 RPM	192.74 RPM
bodymap2_white_blood_cells	0.00 RPM	179.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1724 was not detected

EST

No EST(s) were mapped for retro_hsap_1724 retrocopy.

TSS

No TSS is located nearby retro_hsap_1724 retrocopy 5' end.

Lab

retro_hsap_1724 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1724 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000083312	2 retrocopies	retro_hsap_1724 , retro_hsap_1813,
Mus musculus	ENSMUSG00000009470	1 retrocopy	retro_mmus_1501,
Pongo abelii	ENSPPYG00000015545	1 retrocopy	retro_pabe_1528,
Pan troglodytes	ENSPTRG00000016972	2 retrocopies	retro_ptro_1176, retro_ptro_3060,
Tursiops truncatus	ENSTTRG00000000209	1 retrocopy	retro_ttru_1345,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 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	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 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	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 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:

The presence of retro_hsap_1724 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1724 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	17:18351500..18465800	75.41	88.64	83.51	64.39	70	65	55.88	67.86	52.25	53.76	59.18	92.7	87.11	94.5

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Indel #1, located at the genomic coordinates 17:18351500..18465800.