RetrogeneDB ID: retro_hsap_2045

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:23309376..23310530(-)
• Located in intron of: ENSG00000183850

Retrocopy information

• Ensembl ID: ENSG00000267920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNX32
• Ensembl ID: ENSG00000172803
• Aliases: SNX32, SNX6B
• Description: sorting nexin 32 [Source:HGNC Symbol;Acc:26423]

Sequence

>retro_hsap_2045
AATGTAGATCTTCAAAGTGATCCTGCTCTGCTGGTGGACATTTCTGATGCTCTTAGTGAGCGGAATAAAGTAAAATTCAC
CATTCACACAAAGAGTTTATTGCCAAATTTTAAACAAAATGAGTTTTCTGTTGTTCAGCAACATGAGCAATTTATCTGGC
TTCATGATTCCTTTGTTAAAAATGAAGACTATGCAGGTTACATCATTCCACCAGCACCACCAAGAGCTGATTTTGATGCT
TCAAGGGAAAAAGTACAGAAGCTTGGAGAAGGAGAAGGGTCAATGACAAAGGAAGAATTCACAAAGATGAAACAGGAACT
GGAAGCTGAATATTTGGGAATATCCAAGAACACAGTTGTGATGCATGAAGTGTTCCTATGTCATGTGACAGCACATCCTA
TTTTGAGAAAATATTTAAATTTCCATGTCTTCTTGGAATATAATCAAGATTTGAGTGTGCAAGGAAAAATAAAAAGAGAA
ACTTGAAGATTTCTTTAAAAACATGGTTAAATCAGCAGATGGAGTAATTATTTCCGGAGTAAAGGATGTAGATAATTTCT
TTGAGCATGAACAAACATTTCTTTTAGAATATCATAACCGAGATAAGGATGCATCTGCTAACTCATAGAAGGACAAGATC
CCACAAAAGTGCTGCAGATTATTACAATAGAATTGGTTCTTCATTATATGCTTTAGGAACTCGGGATTCTACAGATATAC
GCAAGTTTTTTCTCAAAGTTTCAGAAATGTTTGATAAAACAAGAAAAATAGAAGCATGAGTGTCTGCTGATGAGGACCTC
AAACTTTCTGACCCTTAAAAATATTACTTAAGAGAAACTCAAGCTGCTAAGGATCTCCTGTATTGAAGGTCTAGGTCACT
ACTGGATTATGAAAATGCTAATATAGCACTGGATAAAGCAAGAGCAAAAAATAAAGATGTTCTGCTGGCTAAAACTTCCC
AACAATTATGTAGTCAGAAATTTGAAAAAAAAAAATCTCAGTCTGCAAAACAAGAACTTATAGATTTTAAGACAAGAAGC
ATTGCTGCATTCAGAAAAAAAAAAAAACTAGTGGAACTGGCAGAGTTAGAACTGAAGCATGCAAAGGGTAACCTACAGTT
GCTGCCAAACTGCCTGGCAGTGCTAAACGGAGAC

Alignment

ORF - retro_hsap_2045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.97 %
• Parental protein coverage: 95.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVDLQGDSSLQVEISDAVSERDKVKFTVQTKSCLPHFAQTEFSVVRQHEEFIWLHDAYVENEEYAGLIIP
          .VDLQ.D..L.V.ISDA.SER.KVKFT..TKS.LP.F.Q.EFSVV.QHE.FIWLHD..V.NE.YAG.IIP
Retrocopy NVDLQSDPALLVDISDALSERNKVKFTIHTKSLLPNFKQNEFSVVQQHEQFIWLHDSFVKNEDYAGYIIP

Parental  PAPPRPDFEASREKLQKLGEGDSSVTREEFAKMKQELEAEYLAIFKKTVAMHEVFLQRLAAHPTLRRDHN
          PAPPR.DF.ASREK.QKLGEG..S.T.EEF.KMKQELEAEYL.I.K.TV.MHEVFL....AHP.LR...N
Retrocopy PAPPRADFDASREKVQKLGEGEGSMTKEEFTKMKQELEAEYLGISKNTVVMHEVFLCHVTAHPILRKYLN

Parental  FFVFLEYGQDLSVRG-KNRK-ELLGGFLRNIVKSADEALITGMSGLKEVDDFFEHERTFLLEYH-TRIRD
          F.VFLEY.QDLSV.G.KN.K.E.L..F..N.VKSAD...I...SG.K.VD.FFEHE.TFLLEYH.T.IR.
Retrocopy FHVFLEYNQDLSVQG<KNKK<EKLEDFFKNMVKSADGVII---SGVKDVDNFFEHEQTFLLEYH>TEIRM

Parental  ACLRADRVMRAHKCLADDYIPISAALSSLGTQEVNQLRTSFLKLAELFERLRKLEGRVASDEDLKLSDML
          ..L...R..R.HK..AD.Y..I...L..LGT......R..FLK..E.F...RK.E..V..DEDLKLSD..
Retrocopy HLLTHRRT-RSHKSAADYYNRIGSSLYALGTRDSTDIRKFFLKVSEMFDKTRKIEA*VSADEDLKLSDP*

Parental  RYYMRDSQAAKDLLYRRLRALADYENANKALDKARTRNREVRPAESHQQLCCQRF-ERLSDSAKQELMDF
          .YY.R..QAAKDLLY.R.R.L.DYENAN.ALDKAR..N..V..A...QQLC.Q.F....S.SAKQEL.DF
Retrocopy KYYLRETQAAKDLLY*RSRSLLDYENANIALDKARAKNKDVLLAKTSQQLCSQKFXXXXSQSAKQELIDF

Parental  KSRRVSSF--RKNLIELAELELKHAKASTLILRNTLVALKGE
          K.R....F.....L.ELAELELKHAK.....L.N.L..L.G.
Retrocopy KTRSIAAFXXXXXLVELAELELKHAKGNLQLLPNCLAVLNGD

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	0.56 RPM
bodymap2_adrenal	0.00 RPM	4.79 RPM
bodymap2_brain	0.00 RPM	9.63 RPM
bodymap2_breast	0.12 RPM	1.50 RPM
bodymap2_colon	0.00 RPM	1.55 RPM
bodymap2_heart	0.00 RPM	0.11 RPM
bodymap2_kidney	0.00 RPM	0.74 RPM
bodymap2_liver	0.00 RPM	0.23 RPM
bodymap2_lung	0.00 RPM	0.42 RPM
bodymap2_lymph_node	0.00 RPM	1.96 RPM
bodymap2_ovary	0.08 RPM	1.23 RPM
bodymap2_prostate	0.00 RPM	0.52 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.18 RPM
bodymap2_testis	0.04 RPM	2.88 RPM
bodymap2_thyroid	0.04 RPM	1.00 RPM
bodymap2_white_blood_cells	0.00 RPM	0.79 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2045 was not detected

EST

No EST(s) were mapped for retro_hsap_2045 retrocopy.

TSS

No TSS is located nearby retro_hsap_2045 retrocopy 5' end.

Lab

retro_hsap_2045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2045 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Homo sapiens	ENSG00000172803	1 retrocopy	retro_hsap_2045 ,
Gorilla gorilla	ENSGGOG00000010801	1 retrocopy	retro_ggor_1473,
Macaca mulatta	ENSMMUG00000019017	1 retrocopy	retro_mmul_1395,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.09 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.16 RPM
GBR_HG00119	0.10 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.17 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.19 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.16 RPM

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Indel association:

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