RetrogeneDB ID: retro_hsap_4759

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:133406316..133407432(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000214961
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NT5DC1
• Ensembl ID: ENSG00000178425
• Aliases: None
• Description: 5'-nucleotidase domain containing 1 [Source:HGNC Symbol;Acc:21556]

Sequence

>retro_hsap_4759
ATGGCTCAGCACTTCTCCCTGGACGCCTGCGATGTGGTCGGATTCTACCTGGACCACACCCTGTGTCACTACAACCTGCC
CGAGAGCGCCCCACTCATTTATAATAGCTTTGCCCAGTTCTTAGTTAAGGAGAAAGGGTATGATAAGGAATTGCTCAATG
TGACCCCAGAGGATTGGAATTTCTGTTGCAAGGGTTTGGCATTGGATCTAGAAGATAGGAACTTCCTTAAACTTGCTGAT
AATGGCACTGTTCTCAGGGCAAGCCATGGCACCAAGATGATGACTCCAGAGGTGCTGGCAGAGACATATGGCAAGAAAGG
GTGGAAGCATTTCTTGTCGGACACTGGAATGGCTTGCCGCTCATGAAAGTATTATTTTTACAACTACTTTGACCTGCCGG
GAGCTCTTCTATGTGCCAGGGTGGTGGACTATTTAACAACAAACAATGGTCAAAAAACATTTGATTTTTGGAAGGATATA
GTTGCTGCTATACAACACAATTATAAAATGTCAGCTTTTAAGGAAAACTGTGGAATATATATTCCAGAAGTAAAAAGAGA
TCCAGGCAGATATTTACACAGTTGTCCTAAATCTGTGAAAAAATGGCTTCGACAGCTAAAGAATGCTGGGAAAATTCTTC
TGTTAATTACCAGTTCTCACAGTGATTACTGTAGACTTCTCTGCGAATATATCCTCGGGAATGATTTTGCAGACCTTTTT
GACATTGTGATTACAAATGCATTGAAGCCTGGTTTCTTCTCCCACTTACCAAGTCAGAGACCTTTCTGGATGCAGAGAAT
GATGAGGAGCAGGAGGCGCTGCCATCTCTGGATAAACCTGGCTGGTGCTCCCAAGGGAACGCTATCCACCTCTATGAACT
TCTGAAGAAAATCAATGGCAAACCTGAACCCAAGGTTGTTTATTACGGCATGCATTCAGATATTTTCCTGGCTCATCACT
ATAGTAATTGGGAGACAGTTCTTATCCTGGAAGAACTCAGAGGGATGAAGGTGCAAGGAGTCAGAGGCCTGAGAAGTCAG
AGCCTCTAGAGAAAAAGGAAAATATGAGGGACCAAAGGTAAAGCCTCTAAATACTTCATCTAAAAAATGAGGCTCC

Alignment

ORF - retro_hsap_4759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.79 %
• Parental protein coverage: 82.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQHFSLAACDVVGFDLDHTLCRYNLPESAPLIYNSFAQFLVKEKGYDKELLNVTPEDWDFCCKGLALDL
          MAQHFSL.ACDVVGF.LDHTLC.YNLPESAPLIYNSFAQFLVKEKGYDKELLNVTPEDW.FCCKGLALDL
Retrocopy MAQHFSLDACDVVGFYLDHTLCHYNLPESAPLIYNSFAQFLVKEKGYDKELLNVTPEDWNFCCKGLALDL

Parental  EDGNFLKLANNGTVLRASHGTKMMTPEVLAEAYGKKEWKHFLSDTGMACRSGKYYFYDNYFDLPGALLCA
          ED.NFLKLA.NGTVLRASHGTKMMTPEVLAE.YGKK.WKHFLSDTGMACRS.KYYFY.NYFDLPGALLCA
Retrocopy EDRNFLKLADNGTVLRASHGTKMMTPEVLAETYGKKGWKHFLSDTGMACRS*KYYFY-NYFDLPGALLCA

Parental  RVVDYLTKLNNGQKTFDFWKDIVAAIQHNYKMSAFKENCGIYFPEIKRDPGRYLHSCPESVKKWLRQLKN
          RVVDYLT..NNGQKTFDFWKDIVAAIQHNYKMSAFKENCGIY.PE.KRDPGRYLHSCP.SVKKWLRQLKN
Retrocopy RVVDYLT-TNNGQKTFDFWKDIVAAIQHNYKMSAFKENCGIYIPEVKRDPGRYLHSCPKSVKKWLRQLKN

Parental  AGKILLLITSSHSDYCRLLCEYILGNDFTDLFDIVITNALKPGFFSHLPSQRP-FRTLENDEEQEALPSL
          AGKILLLITSSHSDYCRLLCEYILGNDF.DLFDIVITNALKPGFFSHLPSQRP.F...ENDEEQEALPSL
Retrocopy AGKILLLITSSHSDYCRLLCEYILGNDFADLFDIVITNALKPGFFSHLPSQRP<FLDAENDEEQEALPSL

Parental  DKPGWYSQGNAVHLYELLKKMTGKPEPKVVYFGDSMHSDIFPARHYSNWETVLILEELRG-DEGTRSQRP
          DKPGW.SQGNA.HLYELLKK..GKPEPKVVY.G..MHSDIF.A.HYSNWETVLILEELRG.DEG.RSQRP
Retrocopy DKPGWCSQGNAIHLYELLKKINGKPEPKVVYYG--MHSDIFLAHHYSNWETVLILEELRG<DEGARSQRP

Parental  EESEPLEK-KGKYEGPKAKPLNTSSKKWGS
          E.SEPLEK.KGKYEGPK.KPLNTSSKK.GS
Retrocopy EKSEPLEK<KGKYEGPKVKPLNTSSKK*GS

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	0.12 RPM	29.52 RPM
bodymap2_adrenal	0.00 RPM	47.39 RPM
bodymap2_brain	0.21 RPM	52.58 RPM
bodymap2_breast	0.04 RPM	42.08 RPM
bodymap2_colon	0.00 RPM	32.56 RPM
bodymap2_heart	0.06 RPM	54.46 RPM
bodymap2_kidney	0.27 RPM	48.45 RPM
bodymap2_liver	0.06 RPM	25.92 RPM
bodymap2_lung	0.05 RPM	25.37 RPM
bodymap2_lymph_node	0.27 RPM	30.92 RPM
bodymap2_ovary	0.00 RPM	37.78 RPM
bodymap2_prostate	0.23 RPM	55.10 RPM
bodymap2_skeletal_muscle	0.27 RPM	37.45 RPM
bodymap2_testis	0.00 RPM	48.51 RPM
bodymap2_thyroid	0.08 RPM	56.72 RPM
bodymap2_white_blood_cells	0.28 RPM	47.39 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4759 was not detected

EST

No EST(s) were mapped for retro_hsap_4759 retrocopy.

TSS

No TSS is located nearby retro_hsap_4759 retrocopy 5' end.

Lab

retro_hsap_4759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4759 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3170
Pongo abelii	retro_pabe_3703

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000178425	1 retrocopy	retro_hsap_4759 ,
Myotis lucifugus	ENSMLUG00000008313	1 retrocopy	retro_mluc_306,
Nomascus leucogenys	ENSNLEG00000013080	1 retrocopy	retro_nleu_2344,
Pongo abelii	ENSPPYG00000016943	1 retrocopy	retro_pabe_3703,
Pan troglodytes	ENSPTRG00000018523	1 retrocopy	retro_ptro_3170,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.05 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	0.03 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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