RetrogeneDB ID:

retro_hsap_2047

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:28296334..28296933(-)
Located in intron of:ENSG00000267575
Retrocopy
information
Ensembl ID:ENSG00000267323
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A1
Ensembl ID:ENSG00000268928
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 [Source:HGNC Symbol;Acc:10979]


Retrocopy-Parental alignment summary:






>retro_hsap_2047
TTCCTCAGCAACCAGATGCGGGATGCCCAGGGACTGGTGAACAGCAAGGCGGGCAGCGGTGCGGCCAGTGAGCTAGCGTG
GCCGAGGCCGTGGTGGTCCTATGTCCCATGGAGACCATCAAGGTGAAGTTAATCCATGGCCAGACCTCTCCAAATCCAAG
TACAGGGGATTCTTCCACAGGGTTAGGAGATTGTGCGGGAACACCGGGACTTACCGGGGCCCCACAGGCCCCGTGCTGAA
GCAGGGCTGGAACCAGGCAACTTGTTTCTTTGTCCTGACATCCCTGCGCAGCTGGTACCGAGTGGACAGCCCCAACAAAC
TCATGAACCCGCTGGTCGCTGGGTTCTTCGGAGCCATTGTGGGAGCGGCCAGTGTCTTCGGAAATGCTCCTCTGCACGAG
ATCGAGCCCCAGATGCGAGACCTGGAGGTGCACAAATGCAGAACACATGGGACTGTGGCTGCAAATCCTGAGGGAAGGGC
ACAAGACCTTCTACAAGGGCACTATTGCCTGCCTGGGCCGGGTCTGCCTGCATGTGGCCATAGTGTTTATCATCTATGAT
GAGGTGAGGAAGCTGCTCAACAAAGTGTGGAAGACAGAG

ORF - retro_hsap_2047 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.38 %
Parental protein coverage: 65.92 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalFLSNHMRDAQGRLDSTRGL-LCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPNP-KYRGFFHGVREIVRE
FLSN.MRDAQG...S..G...CG..A.VAEAVVV.CPMETIKVK.IH.QTSPNP.KYRGFFH.VR.....
RetrocopyFLSNQMRDAQGLVNSKAGS<RCGQ*ASVAEAVVVLCPMETIKVKLIHGQTSPNP<KYRGFFHRVRRLC--
ParentalQGLKGTYQGLTATVLKQGSNQAIRFFVMTSLRNWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVI
.G..GTY.G.T..VLKQG.NQA..FFV.TSLR.WYR.D.PNK.MNPL..G.FGAI.GAASVFGN.PL..I
Retrocopy-GNTGTYRGPTGPVLKQGWNQATCFFVLTSLRSWYRVDSPNKLMNPLVAGFFGAIVGAASVFGNAPLHEI
ParentalKTRMQGLEAHKYR-NTWDCG-LQILKKEGLKAFYKGTVPRLGRVCLDVAIVFVIYDEVVKLLNKVWKTD
...M..LE.HK.R.NTWDCG.LQIL..EG.K.FYKGT...LGRVCL.VAIVF.IYDEV.KLLNKVWKT.
RetrocopyEPQMRDLEVHKCR<NTWDCG<LQIL-REGHKTFYKGTIACLGRVCLHVAIVFIIYDEVRKLLNKVWKTE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .40 RPM 0 .00 RPM
bodymap2_adrenal 0 .74 RPM 0 .00 RPM
bodymap2_brain 0 .19 RPM 0 .00 RPM
bodymap2_breast 0 .47 RPM 0 .00 RPM
bodymap2_colon 1 .80 RPM 0 .00 RPM
bodymap2_heart 0 .90 RPM 0 .00 RPM
bodymap2_kidney 1 .37 RPM 0 .00 RPM
bodymap2_liver 0 .11 RPM 0 .00 RPM
bodymap2_lung 0 .84 RPM 0 .00 RPM
bodymap2_lymph_node 2 .01 RPM 0 .00 RPM
bodymap2_ovary 0 .75 RPM 0 .00 RPM
bodymap2_prostate 1 .54 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .11 RPM 0 .00 RPM
bodymap2_testis 0 .64 RPM 0 .00 RPM
bodymap2_thyroid 1 .07 RPM 0 .00 RPM
bodymap2_white_blood_cells 1 .38 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2047 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2047 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2047 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2047 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2047 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1364
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000268928 1 retrocopy
retro_hsap_2047 ,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 2.81 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .48 RPM
CEU_NA11843 1 .88 RPM
CEU_NA11930 1 .73 RPM
CEU_NA12004 1 .63 RPM
CEU_NA12400 1 .68 RPM
CEU_NA12751 1 .63 RPM
CEU_NA12760 1 .98 RPM
CEU_NA12827 1 .23 RPM
CEU_NA12872 1 .58 RPM
CEU_NA12873 2 .23 RPM
FIN_HG00183 1 .67 RPM
FIN_HG00277 1 .63 RPM
FIN_HG00315 1 .35 RPM
FIN_HG00321 1 .69 RPM
FIN_HG00328 1 .11 RPM
FIN_HG00338 1 .32 RPM
FIN_HG00349 1 .85 RPM
FIN_HG00375 2 .40 RPM
FIN_HG00377 1 .13 RPM
FIN_HG00378 1 .57 RPM
GBR_HG00099 2 .32 RPM
GBR_HG00111 1 .44 RPM
GBR_HG00114 2 .81 RPM
GBR_HG00119 1 .32 RPM
GBR_HG00131 1 .47 RPM
GBR_HG00133 1 .81 RPM
GBR_HG00134 2 .49 RPM
GBR_HG00137 1 .32 RPM
GBR_HG00142 1 .97 RPM
GBR_HG00143 2 .07 RPM
TSI_NA20512 1 .61 RPM
TSI_NA20513 2 .25 RPM
TSI_NA20518 1 .39 RPM
TSI_NA20532 1 .63 RPM
TSI_NA20538 2 .03 RPM
TSI_NA20756 2 .12 RPM
TSI_NA20765 1 .64 RPM
TSI_NA20771 2 .35 RPM
TSI_NA20786 1 .57 RPM
TSI_NA20798 1 .96 RPM
YRI_NA18870 1 .25 RPM
YRI_NA18907 1 .56 RPM
YRI_NA18916 1 .54 RPM
YRI_NA19093 1 .67 RPM
YRI_NA19099 1 .68 RPM
YRI_NA19114 1 .60 RPM
YRI_NA19118 1 .18 RPM
YRI_NA19213 1 .05 RPM
YRI_NA19214 1 .35 RPM
YRI_NA19223 1 .11 RPM

Indel association:

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



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