RetrogeneDB ID: retro_hsap_3273

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:177398320..177399279(+)
• Located in intron of: ENSG00000250101

Retrocopy information

• Ensembl ID: ENSG00000249129
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUDS3
• Ensembl ID: ENSG00000111707
• Aliases: SUDS3, SAP45, SDS3
• Description: suppressor of defective silencing 3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29545]

Sequence

>retro_hsap_3273
GCGCCGCGGGGCTGCTGGCCCCGGCCCCGCCCGGGCTGGAGCGTCCCCGGGGAGGACGAAGAGCTGGAGAGCGCCAAGGA
CGACGAGCGCAGCTGCCGGGCCGCGAGTCGGACGAAGACACTGAGGATGCTAGTGAAACTGACCTGGCAAAGCATGATGA
AGAAGACTATGGGGAAGTGAAGGAACAGATGTATCAGGACAAACTGGCTTCTCTCGAGAGGCAGTTGCAACAACTACAAG
AAGGTACATTACAGGAATATCAGAAGAGAATGAAAAAACTAGGTCAGCAGTACAAAGAGAGGATACGGAATGCTGAACTC
TTCCTCCAGCTGGAAACTGAACAAGTGGGACGAAATTACATGAAAGAAAAGAAGGCAGCAGTGAAAGAATTTGAAGACAA
GAAGGTTGAGCTGAAAGAGAACCTGATTGCTGAGCTAGCAGAAGAGAAGAAAATGATTGAAAACGAAATGCTGACAATGG
AACTGAATGGAGATTCTATGCAGGTGAGACCTATCATGACCAGAAAGTTGCGGAGGCGACCAAATGATCCCGTCCCCATC
CCAGACAAGAGGAGGAAACCTGCTCCAGCCCAGCTAAACTATTTGTTAACAGATGAACAGATCATGGAGGATCTGAGAAC
ATTAAATAAGCTTAAGTCACCCAAGAGACCAGCATCTCCATCCTCTCCTGAGCACTTGCCTGCGACACCCGCGGAATCTC
CAGCCCAGAGGTTTGAAGCTCGGATAGAAGATGGCAAACTGCACTATGACAAAAGATGGTACCACAAGAGCCAGGCCATC
TATCTGGAGTCAAAGGACAACCAGAAACTGAGCTGCGTGATCAGTTCTGTAGGAGCCAATGAGATCTGGGTGAGGAAGAC
AAGTGACAGCACCAAGATGAGGATCTACCTGGGCCAGCTTCAGCGCGGGCTCTTCGTCATCCACCGGCGCTCAGCTGCT

Alignment

ORF - retro_hsap_3273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 97.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APAQAGAPPAPEY-YPEEDEELESAEDDERSCR-GRESDEDTEDASETDLAKHDEEDYVEMKEQMYQDKL
          AP......P.P....P.EDEELESA.DDERSCR.GRESDEDTEDASETDLAKHDEEDY.E.KEQMYQDKL
Retrocopy APRGCWPRPRPGWSVPGEDEELESAKDDERSCR<GRESDEDTEDASETDLAKHDEEDYGEVKEQMYQDKL

Parental  ASLKRQLQQLQEGTLQEYQKRMKKLDQQYKERIRNAELFLQLETEQVERNYIKEKKAAVKEFEDKKVELK
          ASL.RQLQQLQEGTLQEYQKRMKKL.QQYKERIRNAELFLQLETEQV.RNY.KEKKAAVKEFEDKKVELK
Retrocopy ASLERQLQQLQEGTLQEYQKRMKKLGQQYKERIRNAELFLQLETEQVGRNYMKEKKAAVKEFEDKKVELK

Parental  ENLIAELEEKKKMIENEKLTMELTGDSMEVKPIMTRKLRRRPNDPVPIPDKRRKPAPAQLNYLLTDEQIM
          ENLIAEL.E.KKMIENE.LTMEL.GDSM.V.PIMTRKLRRRPNDPVPIPDKRRKPAPAQLNYLLTDEQIM
Retrocopy ENLIAELAEEKKMIENEMLTMELNGDSMQVRPIMTRKLRRRPNDPVPIPDKRRKPAPAQLNYLLTDEQIM

Parental  EDLRTLNKLKSPKRPASPSSPEHLPATPAESPAQRFEARIEDGKLYYDKRWYHKSQAIYLESKDNQKLSC
          EDLRTLNKLKSPKRPASPSSPEHLPATPAESPAQRFEARIEDGKL.YDKRWYHKSQAIYLESKDNQKLSC
Retrocopy EDLRTLNKLKSPKRPASPSSPEHLPATPAESPAQRFEARIEDGKLHYDKRWYHKSQAIYLESKDNQKLSC

Parental  VISSVGANEIWVRKTSDSTKMRIYLGQLQRGLFVIRRRSAA
          VISSVGANEIWVRKTSDSTKMRIYLGQLQRGLFVI.RRSAA
Retrocopy VISSVGANEIWVRKTSDSTKMRIYLGQLQRGLFVIHRRSAA

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	0.52 RPM	44.80 RPM
bodymap2_adrenal	0.04 RPM	45.85 RPM
bodymap2_brain	0.33 RPM	32.68 RPM
bodymap2_breast	0.64 RPM	47.90 RPM
bodymap2_colon	0.50 RPM	67.85 RPM
bodymap2_heart	0.07 RPM	33.43 RPM
bodymap2_kidney	0.52 RPM	60.90 RPM
bodymap2_liver	0.28 RPM	18.57 RPM
bodymap2_lung	0.23 RPM	48.70 RPM
bodymap2_lymph_node	0.22 RPM	56.58 RPM
bodymap2_ovary	0.44 RPM	73.56 RPM
bodymap2_prostate	0.52 RPM	86.81 RPM
bodymap2_skeletal_muscle	0.04 RPM	28.83 RPM
bodymap2_testis	1.28 RPM	71.60 RPM
bodymap2_thyroid	1.49 RPM	65.98 RPM
bodymap2_white_blood_cells	0.69 RPM	63.89 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3273 was not detected

EST

No EST(s) were mapped for retro_hsap_3273 retrocopy.

TSS

No TSS is located nearby retro_hsap_3273 retrocopy 5' end.

Lab

retro_hsap_3273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3273 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000111707	1 retrocopy	retro_hsap_3273 ,
Loxodonta africana	ENSLAFG00000001274	1 retrocopy	retro_lafr_248,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.26 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.20 RPM
CEU_NA12004	0.19 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.39 RPM
CEU_NA12760	0.45 RPM
CEU_NA12827	0.28 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.29 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.48 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.27 RPM
FIN_HG00328	0.19 RPM
FIN_HG00338	0.21 RPM
FIN_HG00349	0.17 RPM
FIN_HG00375	0.44 RPM
FIN_HG00377	0.30 RPM
FIN_HG00378	0.34 RPM
GBR_HG00099	0.29 RPM
GBR_HG00111	0.28 RPM
GBR_HG00114	0.29 RPM
GBR_HG00119	0.29 RPM
GBR_HG00131	0.46 RPM
GBR_HG00133	0.29 RPM
GBR_HG00134	0.35 RPM
GBR_HG00137	0.22 RPM
GBR_HG00142	0.19 RPM
GBR_HG00143	0.26 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.41 RPM
TSI_NA20518	0.28 RPM
TSI_NA20532	0.31 RPM
TSI_NA20538	0.55 RPM
TSI_NA20756	0.29 RPM
TSI_NA20765	0.37 RPM
TSI_NA20771	0.48 RPM
TSI_NA20786	0.29 RPM
TSI_NA20798	0.31 RPM
YRI_NA18870	0.30 RPM
YRI_NA18907	0.35 RPM
YRI_NA18916	0.34 RPM
YRI_NA19093	0.60 RPM
YRI_NA19099	0.51 RPM
YRI_NA19114	0.29 RPM
YRI_NA19118	0.21 RPM
YRI_NA19213	0.45 RPM
YRI_NA19214	0.25 RPM
YRI_NA19223	0.48 RPM

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Indel association:

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