RetrogeneDB ID:

retro_hsap_804

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:85645779..85646693(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254479
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A1
Ensembl ID:ENSG00000100075
Aliases:SLC25A1, CTP, D2L2AD, SEA, SLC20A3
Description:solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 [Source:HGNC Symbol;Acc:10979]


Retrocopy-Parental alignment summary:






>retro_hsap_804
GCGCCTCGAGCCCCACACGCTCTGGCGGCCGCCGCGCCAGCGTCTGGGAAGGCCAAGCTGACGCACCTGGGGAAGGCGAT
CCTGGCAGGCGGCCTGGCGGGCGGCATTGAGATCTACATCACCTTCCCCACCCAGTACGTGAAGACGCAGTGGCAGCTGG
ACTAGCCCTCGAACCCGCCGCGGTACCAGAGCATCGGGGAGTGGGTGTGGCAGACAGTCCGCAGCCATGGCGTTCTGGGC
CTGTACCGCAGTCTCAGCTCCCTGCTCTACGGCTCCATCCCCAAAGCGGCCGCCAGCTTCGGAATGTTCTAGTTCCTCGG
CAACCACCTGCGGGATTCCCAGGGACGGCTGGACAGCACGCGCGGGCTGCTGTGCTGCCTGGGCGCTGGAGTGGCTGAGG
CCGTGGTGATCGTGTGCCCCATGGAGACCATCAAGGTGAGGTTCATCCACGACCAGACCTCCCCAAACCCCAAGTACCGA
GGATTCTTCTACGGGTTAGGAAGATTGTGCGGGAACAAGGGCTGAAGGGGATGTATCAGAGCCTCACGGCCACCGTACTG
AAACAGGGCTGGAACCAGGCCATCCGCTTCTTCGTCATGACATTCCCTGCACAACTGGTACCGAGGAGACAACCCCAACA
AGCCCATGAACCCGCTGATCACTGGGGGCTTCGGAGCCATCGTGTGCACAGCCAGCGTCTTTGGAAACACTCCTCTGGAC
GTGATTAAGACCCGCAGGTAGGGCCTGGAGGCGCACAAATACCGGAACTTGATGGACTGTGGCTGGCAGATCCTGAGGAA
GGAGGAGCTCAAGGCATTCTACAAGGGCATTGTCCCGCGCTGGGCCAGGTCAACCTGGATGTGGCCATAGTGTTTATCAT
CTATGATGAGGTGGTGAAGCTGCTCAACAAAGTG

ORF - retro_hsap_804 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.74 %
Parental protein coverage: 98.07 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalAPRAPRALAAAAPASGKAKLTHPGKAILAGGLAGGIEICITFPTEYVKTQLQLDERSHPPRYRGIGDCVR
APRAP.ALAAAAPASGKAKLTH.GKAILAGGLAGGIEI.ITFPT.YVKTQ.QLD..S.PPRY..IG..V.
RetrocopyAPRAPHALAAAAPASGKAKLTHLGKAILAGGLAGGIEIYITFPTQYVKTQWQLD*PSNPPRYQSIGEWVW
ParentalQTVRSHGVLGLYRGLSSLLYGSIPKAAVRFGMFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCP
QTVRSHGVLGLYR.LSSLLYGSIPKAA..FGMF.FL.NH.RD.QGRLDSTRGLLC.LGAGVAEAVV.VCP
RetrocopyQTVRSHGVLGLYRSLSSLLYGSIPKAAASFGMF*FLGNHLRDSQGRLDSTRGLLCCLGAGVAEAVVIVCP
ParentalMETIKVKFIHDQTSPNPKYRGFFHG-VREIVREQGLKGTYQGLTATVLKQGSNQAIRFFVMT-SLRNWYR
METIKV.FIHDQTSPNPKYRGFF.G.VR.IVREQGLKG.YQ.LTATVLKQG.NQAIRFFVMT.SL.NWYR
RetrocopyMETIKVRFIHDQTSPNPKYRGFFYG<VRKIVREQGLKGMYQSLTATVLKQGWNQAIRFFVMT>SLHNWYR
ParentalGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWDCGLQILKKEGLKAFYKGTV
GDNPNKPMNPLITG.FGAI...ASVFGNTPLDVIKTR..GLEAHKYRN..DCG.QIL.KE.LKAFYKG.V
RetrocopyGDNPNKPMNPLITGGFGAIVCTASVFGNTPLDVIKTRR*GLEAHKYRNLMDCGWQILRKEELKAFYKGIV
ParentalPR-LGRVCLDVAIVFVIYDEVVKLLNKV
PR.LG.V.LDVAIVF.IYDEVVKLLNKV
RetrocopyPR<LGQVNLDVAIVFIIYDEVVKLLNKV

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 .02 RPM 54 .49 RPM
bodymap2_adrenal 0 .02 RPM 30 .62 RPM
bodymap2_brain 0 .02 RPM 12 .59 RPM
bodymap2_breast 0 .04 RPM 92 .04 RPM
bodymap2_colon 0 .00 RPM 30 .92 RPM
bodymap2_heart 0 .00 RPM 7 .86 RPM
bodymap2_kidney 0 .00 RPM 38 .76 RPM
bodymap2_liver 0 .00 RPM 53 .46 RPM
bodymap2_lung 0 .00 RPM 30 .10 RPM
bodymap2_lymph_node 0 .00 RPM 34 .52 RPM
bodymap2_ovary 0 .00 RPM 39 .59 RPM
bodymap2_prostate 0 .00 RPM 44 .63 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .37 RPM
bodymap2_testis 0 .06 RPM 38 .18 RPM
bodymap2_thyroid 0 .04 RPM 31 .71 RPM
bodymap2_white_blood_cells 0 .02 RPM 20 .99 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_804 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_804 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_804 retrocopy 5' end.

Lab - click to see more details

retro_hsap_804 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_804 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_560
Gorilla gorilla retro_ggor_661
Pongo abelii retro_pabe_719
Macaca mulatta retro_mmul_1077
Parental genes homology:
Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000100075 2 retrocopies
retro_hsap_1632, retro_hsap_804 ,
Gorilla gorilla ENSGGOG000000061982 retrocopies
retro_ggor_1230, retro_ggor_661,
Macaca mulatta ENSMMUG000000054314 retrocopies
retro_mmul_1077, retro_mmul_1556, retro_mmul_1683, retro_mmul_485,
Nomascus leucogenys ENSNLEG000000052152 retrocopies
retro_nleu_2866, retro_nleu_408,
Ochotona princeps ENSOPRG000000116491 retrocopy
retro_opri_1053,
Pongo abelii ENSPPYG000000297859 retrocopies
retro_pabe_1346, retro_pabe_1414, retro_pabe_1529, retro_pabe_1671, retro_pabe_3125, retro_pabe_3217, retro_pabe_334, retro_pabe_3564, retro_pabe_719,
Pan troglodytes ENSPTRG000000140573 retrocopies
retro_ptro_1139, retro_ptro_1364, retro_ptro_560,
Tursiops truncatus ENSTTRG000000068451 retrocopy
retro_ttru_228,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 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 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 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

Indel association:

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





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