RetrogeneDB ID:

retro_hsap_3445

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:30436706..30437996(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224936
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SUCLA2
Ensembl ID:ENSG00000136143
Aliases:SUCLA2, A-BETA, MTDPS5, SCS-betaA
Description:succinate-CoA ligase, ADP-forming, beta subunit [Source:HGNC Symbol;Acc:11448]


Retrocopy-Parental alignment summary:






>retro_hsap_3445
CGGACCACACTGCGGGCTGCTGCTCAGGTTCTGGGAAGTTCTGGATTGTTTAATAACCATGGACTCCAAGTACAGCAGCA
ACAGCAAAGGAATCTCTCACTACATGAATACATGAGTATGGAATTATTGCAAGAAACTGGTGTCTCTGTTCCCAAAGGAT
ATGTGGCAAAGTGACCAGATGAAGCTTATGCAATTGCCAAAAAATTAGGTTCAAAAGATGTTGTGATGAAGGCACAGGTT
TTAGCTGGTGGTAGAGGAAAAGGAACATTTGAAAGTGGCCTCAAAGGAGGAGTGAAGATGGTTTTCTCTCCAGAAGAAGC
AAAAGCTGTTCCTTCACAAATGATTAGGAAACAGTTGTTTACCAAGCAAATGGGAGAAAAGGGCAGAATATGCAATCAGG
TATTGGTCTGTGAGTGAAAATATCCCAAGAGAGAGTGCTACTTTGCAATAACAATGGAAAGGTCATTTCAAGGTCTTGTA
TTAATAGGAAGTTTACATAGTGGGGCCAACATTGAAGATGTTGCTGCTGAGACTCCTGAAGCAATAATTAAAGTACCTAT
TGATATTGTAGAAGGTATCAAAGAGGAATAAGCTCTCCAGCTTGCACAGAAGATGGGATTTCCATCTAATATTGTGGCTT
CAGCAGCAGAAAACATGATCAAGCTTTACAGCCTTTTTCTGAAATACGATGCAACCATGATAGAAATAAATTCAATGGTG
GAAGATTCAGATGGAGCTGCATTGTGTAAGGATGCAAAGATCAATTTTGACTCTAATTCAGCCTATCGCCAAAAGAAAAT
GTTTGATCTACAGGACTGGACCCAGGAAGATGAAAGGAACAAAGATGCTGCTAAGGCAGATCTCAACTACACTGGCCTCG
ATGGAAGTATAGGCTGCCTAGTAAATGGTGCTGGTTTGGCTATGGCCACAATGGATATAATAAAACTTCATGGAGAGACT
CCAGCTAATTTCCTTGTTGGTGGTGGTGCTACAGTCCATCAAGTAACAGAAGCATTTAAGCCTATCACTTCAGATAAAAA
GGTACTGGCTATTCTGGTCAACATTTGTGGAGGAATCATGCACTGTGATATTACAGCAAAGGGTATAGTCATGGCAGTAA
AAAGTTTGGAAATTAAAATACCTGTTGTGGTACAGTTACAAGGTACACAAGTTGATGATGTTAAGGCACTAAAAGCAGAC
AGTGGACTTAAAATACTTGCTTGTGATGATTTGGTGGAAGCTGCTAGAGTGCTTGTAAAGCTCTCTGAAATAGTGAAGCA
AAGCAAGCGC

ORF - retro_hsap_3445 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.7 %
Parental protein coverage: 93.09 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRTAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQEAGVSVPKGYVAKSPDEAYAIAKKLG
RT..RAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQE.GVSVPKGYVAK.PDEAYAIAKKLG
RetrocopyRTTLRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQETGVSVPKGYVAK*PDEAYAIAKKLG
ParentalSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCERK
SKDVV.KAQVLAGGRGKGTFESGLKGGVK.VFSPEEAKAV.SQMI.K.LFTKQ.GEKGRICNQVLVCE.K
RetrocopySKDVVMKAQVLAGGRGKGTFESGLKGGVKMVFSPEEAKAVPSQMIRKQLFTKQMGEKGRICNQVLVCE*K
ParentalYPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAESPEAIIKEPIDIEEGIKKEQALQLAQKMGFPPN
YP.RE.YFAITMERSFQG.VLIGS.H.G.NIEDVAAE.PEAIIK.PIDI.EGIK.E.ALQLAQKMGFP.N
RetrocopyYPKRECYFAITMERSFQGLVLIGSLHSGANIEDVAAETPEAIIKVPIDIVEGIKEE*ALQLAQKMGFPSN
ParentalIVESAAENMVKLYSLFLKYDATMIEINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERD
IV.SAAENM.KLYSLFLKYDATMIEIN.MVEDSDGA.LC.DAKINFDSNSAYRQKK.FDLQDWTQEDER.
RetrocopyIVASAAENMIKLYSLFLKYDATMIEINSMVEDSDGAALCKDAKINFDSNSAYRQKKMFDLQDWTQEDERN
ParentalKDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVHQVTEAFKLITSDKKVL
KDAAKA.LNY.GLDG.IGCLVNGAGLAMATMDIIKLHG.TPANFL.VGGGATVHQVTEAFK.ITSDKKVL
RetrocopyKDAAKADLNYTGLDGSIGCLVNGAGLAMATMDIIKLHGETPANFL-VGGGATVHQVTEAFKPITSDKKVL
ParentalAILVNIFGGIMRCDVIAQGIVMAVKDLEIKIPVVVRLQGTRVDDAKALIADSGLKILACDDLDEAARMVV
AILVNI.GGIM.CD..A.GIVMAVK.LEIKIPVVV.LQGT.VDD.KAL.ADSGLKILACDDL.EAAR..V
RetrocopyAILVNICGGIMHCDITAKGIVMAVKSLEIKIPVVVQLQGTQVDDVKALKADSGLKILACDDLVEAARVLV
ParentalKLSEIVTLAKQ
KLSEIV...K.
RetrocopyKLSEIVKQSKR

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 .10 RPM 40 .57 RPM
bodymap2_adrenal 0 .00 RPM 32 .73 RPM
bodymap2_brain 0 .00 RPM 119 .38 RPM
bodymap2_breast 0 .00 RPM 114 .24 RPM
bodymap2_colon 0 .00 RPM 65 .70 RPM
bodymap2_heart 0 .04 RPM 144 .18 RPM
bodymap2_kidney 0 .00 RPM 87 .23 RPM
bodymap2_liver 0 .00 RPM 19 .37 RPM
bodymap2_lung 0 .00 RPM 27 .50 RPM
bodymap2_lymph_node 0 .00 RPM 29 .51 RPM
bodymap2_ovary 0 .02 RPM 54 .82 RPM
bodymap2_prostate 0 .00 RPM 60 .95 RPM
bodymap2_skeletal_muscle 0 .00 RPM 68 .11 RPM
bodymap2_testis 0 .11 RPM 56 .09 RPM
bodymap2_thyroid 0 .04 RPM 79 .37 RPM
bodymap2_white_blood_cells 0 .00 RPM 26 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3445 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3445 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3445 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3445 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3445 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2337
Gorilla gorilla retro_ggor_2327
Pongo abelii retro_pabe_2852
Parental genes homology:
Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146102 retrocopies
retro_acar_26, retro_acar_52,
Callithrix jacchus ENSCJAG000000092782 retrocopies
retro_cjac_1233, retro_cjac_2379,
Cavia porcellus ENSCPOG000000149611 retrocopy
retro_cpor_1113,
Homo sapiens ENSG00000136143 3 retrocopies
retro_hsap_2236, retro_hsap_2281, retro_hsap_3445 ,
Homo sapiens ENSG000001723401 retrocopy
retro_hsap_1044,
Gorilla gorilla ENSGGOG000000082243 retrocopies
retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta ENSMMUG000000075391 retrocopy
retro_mmul_1231,
Mustela putorius furoENSMPUG000000014881 retrocopy
retro_mputfur_768,
Nomascus leucogenys ENSNLEG000000029483 retrocopies
retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii ENSOGAG000000074521 retrocopy
retro_ogar_2196,
Pongo abelii ENSPPYG000000053522 retrocopies
retro_pabe_1939, retro_pabe_2852,
Pan troglodytes ENSPTRG000000058593 retrocopies
retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,

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 = 0.04 RPM Legend:


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 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 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 .02 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 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 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

Indel association:

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





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