RetrogeneDB ID: retro_hsap_3855

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:63369558..63370582(-)
• Located in intron of: ENSG00000226581

Retrocopy information

• Ensembl ID: ENSG00000226342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NMD3
• Ensembl ID: ENSG00000169251
• Aliases: None
• Description: NMD3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24250]

Sequence

>retro_hsap_3855
AAAGCCCCTCTGAGTAAGGAACGGCTTGTGAATGCAGGCTTTGTTTGGACTGAGCCCCATTCTAAGAGATTTAAAGTTAA
ACTGACTCCAGAAAGAGGTGATGAATGGTGCTGTCCTTCAACAAGTGTTTGTGGTGGATTATGCTGTTCAGTCCCAAATA
TGTGGAGATTGCCATAGAGTAGAAGCTAAGGGTTTCTGGAGGGCTGTGATTCAAGTGAGGCAAAAGACTTTGCACAAAAA
AGCTTTCTACTATCTGGAACAGTTAATTCTGAAATATGGAAGGCATCAGAATACACTTCGTATCAAAGAGATTCATGATG
GTCTGGATTTTTATTATTCCTCAAAACCACATGCTCAGAAGATGGTCGAATTTATTCAGTATACAGTTCCCTGTAGATAC
AACGCATCCCAAAGACTGATCTCTCAGGATGTCCATAGTAATACATACAATTACAAAAGCACTTTTTCTGTGGAAATTGT
TCCAATATGCCAGGATTATGTTGTCTGTCTGTCTCCAAAACTGACACAAAGCCTGGGAAATATGAACCAGATTTGTGTGT
GTATTCGAATAACCAGTGCCATTCACCTCATTGATCCAAACACCCTACAAGTTGCAGATATTGATGGCAGCACTTTCTGG
AGTCACTCTTTCAGTAGTTTATGTCACCCCAAACAGCTAGAGGAATTTATTGTGATGAAATGCAGCATAGTCCGAAATAT
AAAACACGGTGCAGATGCTGGAATGATATCAAAAAAGCATACCCTCAGGGAAGTCTGGGTACAGAAGACATCTGAAATGA
ATACAGATAAACAGTATTTTTGTCATACTCATTTGGGACATCTTCTAAATCCTGGAGAGCTGGTGTTAGGGTTTGATTTG
GCCAGCTGCAATTTAAATGATGAGCATGGCAACAAAATGAACTCAGATAGAGTTCCAGATGTGGTATTAATCAAGAAGAA
CTAAGACTGGACCAAACATCAGTGATGTAGAAACTGGAAACTGAAAGAGCTTGCAGGAGAGAGA

Alignment

ORF - retro_hsap_3855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 67.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAPLSKVRLVDAGFVWTE-PHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMCGDCHRVEAKDFWKA
          KAPLSK.RLV.AGFVWTE.P....LK.....QKEVMNGA.LQQVFVVDY.VQSQ.CGDCHRVEAK.FW.A
Retrocopy KAPLSKERLVNAGFVWTE>PILRDLKLN*-LQKEVMNGAVLQQVFVVDYAVQSQICGDCHRVEAKGFWRA

Parental  VIQVRQKTLHKKTFYYLEQLILKYGMHQNTLRIKEIHDGLDFYYSSKQHAQKMVEFLQCTVPCRYKASQR
          VIQVRQKTLHKK.FYYLEQLILKYG.HQNTLRIKEIHDGLDFYYSSK.HAQKMVEF.Q.TVPCRY.ASQR
Retrocopy VIQVRQKTLHKKAFYYLEQLILKYGRHQNTLRIKEIHDGLDFYYSSKPHAQKMVEFIQYTVPCRYNASQR

Parental  LISQDIHSNTYNYKSTFSVEIVPICKDNVVCLSPKLAQSLGNMNQICVCIRVTSAIHLIDPNTLQVADID
          LISQD.HSNTYNYKSTFSVEIVPIC.D.VVCLSPKL.QSLGNMNQICVCIR.TSAIHLIDPNTLQVADID
Retrocopy LISQDVHSNTYNYKSTFSVEIVPICQDYVVCLSPKLTQSLGNMNQICVCIRITSAIHLIDPNTLQVADID

Parental  GSTFWSHPFNSLCHPKQLEEFIVMECSIVQDIKRAAGAGMISKKHTLGEVWVQKTSEMNTDKQYFCRTHL
          GSTFWSH.F.SLCHPKQLEEFIVM.CSIV..IK..A.AGMISKKHTL.EVWVQKTSEMNTDKQYFC.THL
Retrocopy GSTFWSHSFSSLCHPKQLEEFIVMKCSIVRNIKHGADAGMISKKHTLREVWVQKTSEMNTDKQYFCHTHL

Parental  GHLLNPGDLVLGFDLANCNLNDEHVNKMNSDRVPDVVLIKKSYDRTKRQRRRNWKLKELARER
          GHLLNPG.LVLGFDLA.CNLNDEH.NKMNSDRVPDVVLIKK..D.TK.Q..RNWKLKELA.ER
Retrocopy GHLLNPGELVLGFDLASCNLNDEHGNKMNSDRVPDVVLIKKN*DWTKHQ*CRNWKLKELAGER

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	0.18 RPM	60.51 RPM
bodymap2_adrenal	0.14 RPM	47.84 RPM
bodymap2_brain	0.19 RPM	46.88 RPM
bodymap2_breast	0.12 RPM	64.07 RPM
bodymap2_colon	0.12 RPM	66.92 RPM
bodymap2_heart	0.02 RPM	52.17 RPM
bodymap2_kidney	0.19 RPM	62.77 RPM
bodymap2_liver	0.00 RPM	48.35 RPM
bodymap2_lung	0.00 RPM	69.87 RPM
bodymap2_lymph_node	0.11 RPM	37.19 RPM
bodymap2_ovary	0.48 RPM	61.65 RPM
bodymap2_prostate	0.16 RPM	76.24 RPM
bodymap2_skeletal_muscle	0.00 RPM	44.32 RPM
bodymap2_testis	0.43 RPM	53.17 RPM
bodymap2_thyroid	0.11 RPM	60.54 RPM
bodymap2_white_blood_cells	0.10 RPM	47.90 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3855 was not detected

EST

No EST(s) were mapped for retro_hsap_3855 retrocopy.

TSS

No TSS is located nearby retro_hsap_3855 retrocopy 5' end.

Lab

retro_hsap_3855 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3855 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2627

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169251	1 retrocopy	retro_hsap_3855 ,
Pan troglodytes	ENSPTRG00000015586	1 retrocopy	retro_ptro_2627,
Tursiops truncatus	ENSTTRG00000012938	1 retrocopy	retro_ttru_749,

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	0.00 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	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.03 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	0.03 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:

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