RetrogeneDB ID:

retro_hsap_3553

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:7341645..7342742(-)
Located in intron of:ENSG00000164304
Retrocopy
information
Ensembl ID:ENSG00000230570
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ACCSL
Ensembl ID:ENSG00000205126
Aliases:None
Description:1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like [Source:HGNC Symbol;Acc:34391]


Retrocopy-Parental alignment summary:






>retro_hsap_3553
ATGAGTCATCAGTCAGACACCCTTCCTGTGCCATCTGGCCAGATGAGAGGCCAGGTCCTCAGAGACCAGAGCATCTATAC
CCAGCTGTTGAGATGATGCTGCACTTGCGGTAGACCATGAGGGAGTACTTCATGCAGCTGATGAGCAGGCAGGGCCCTGC
CGCTGGAAGAATGGAGGCACACTCAGGCCATCCGTGAGCATGAAGCCCTTCTGGGTCGCTTAATGTGCCAGATGATCCAG
CTCCTATAGTCTGGGGCCATAAGTGGCCTGGAGCTCCAAGTGCCTCTTCCTTCCCAGGACTCTAGGGGTGATGTCAGATA
TGGGCAGGGGGCCCAACTGTCCAGGCAGCCTGATCCAGTTCCCCAACTGAGTGATTGTGAAGCTGCCTTCATCAGCCGTG
ACCTATCCAACTGTGGGATTGACATCTCTGTCTTCTATTAGTCGAGCTTCCAGGACTACAATGCCTACCAAAAAGACAAA
TATCATAAGGACAAGAACACCTTGAGCTTCGTTAACCTTGGCACCAGTGAGAACAAGCTCTGCATAGATCTGATGACTGA
AAGATTGCAAGAAAGTGACACGAACGGCATTGAGGACATCTTGCTGCAGTACCCTGATTGGAGAGGGCACCCGTTCCTGC
AAGAAGAAGTGGCCCAGTTCCTGACCTACTAGTGCAAGGCACCTGCCCGACTTGATCCAGAAAATGTGGTTGTTCTAAAT
GGCTGCTGCTCTGTCTTCTCTGCACTGGCCATGGTTCTGTGTGATCCAAGCGAGGCCTTCCTGGCGCCTGCTCCCTTCTA
TAGTGGCTTTGACTTTAGCTCCTGCCTGTACGTGAAGGTTGAGTTGATTCCTGTCCACCTGGAGAGTGAGATCACTGTTG
CAAACACCCATCTGTTCCACCTTGCTGTGGACAAGTTAGAGGAAGCCCTGCTTAAAGCTAGGCCTGAGAGGAAAAAGGTC
CGAGGCCTTGTGCTAATCAACCCTCAGAATCTTCTGGGTGACATCTACTCCTCAGACTCGCGATGGAATACCTGGAATTT
GCCAAGAGGTATAACCTACATGTGATCATAGATGAGATTTACATGCTATCTGTGTTT

ORF - retro_hsap_3553 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.11 %
Parental protein coverage: 64.44 %
Number of stop codons detected: 4
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMSHRSDTLPVPSGQRRGRVPRDHSIYTQLL-EITLHLQQAMTEHFVQLTSRQG-LSLEERRHTEAICEHE
MSH.SDTLPVPSGQ.RG.V.RD.SIYTQLL.E..LHL...M.E.F.QL.SRQG.L.LEE.RHT.AI.EHE
RetrocopyMSHQSDTLPVPSGQMRGQVLRDQSIYTQLL<EMMLHLR*TMREYFMQLMSRQG>LPLEEWRHTQAIREHE
ParentalALLSRLICRMINLLQSGAASGLELQVPLPSEDSRGDVRYGQRAQLSGQPDPVPQLSDCEAAFVNRDLSIR
ALL.RL.C.MI.LL.SGA.SGLELQVPLPS.DSRGDVRYGQ.AQLS.QPDPVPQLSDCEAAF..RDLS..
RetrocopyALLGRLMCQMIQLL*SGAISGLELQVPLPSQDSRGDVRYGQGAQLSRQPDPVPQLSDCEAAFISRDLSNC
ParentalGIDISVFYQSSFQDYNAYQKDKYHKDKNTLGFINLGTSENKLCMDLMTERLQESDMNCIEDTLLQYPDWR
GIDISVFY.SSFQDYNAYQKDKYHKDKNTL.F.NLGTSENKLC.DLMTERLQESD.N.IED.LLQYPDWR
RetrocopyGIDISVFY*SSFQDYNAYQKDKYHKDKNTLSFVNLGTSENKLCIDLMTERLQESDTNGIEDILLQYPDWR
ParentalGQPFLREEVARFLTYYCRAPTRLDPENVVVLNGCCSVFCALAMVLCDPGEAFLVPAPFYGGFAFSSRLYA
G.PFL.EEVA.FLTY.C.AP.RLDPENVVVLNGCCSVF.ALAMVLCDP.EAFL.PAPFY.GF.FSS.LY.
RetrocopyGHPFLQEEVAQFLTY*CKAPARLDPENVVVLNGCCSVFSALAMVLCDPSEAFLAPAPFYSGFDFSSCLYV
ParentalKVELIPVHLESEVTVTNTHPFQLTVDKLEEALLEARLEGKKVRGLVLINPQNPLGDIYSPDS-LMKYLEF
KVELIPVHLESE.TV.NTH.F.L.VDKLEEALL.AR.E.KKVRGLVLINPQN.LGDIYS.DS..M.YLEF
RetrocopyKVELIPVHLESEITVANTHLFHLAVDKLEEALLKARPERKKVRGLVLINPQNLLGDIYSSDS<AMEYLEF
ParentalAKRYNLHVIIDEIYMLSVF
AKRYNLHVIIDEIYMLSVF
RetrocopyAKRYNLHVIIDEIYMLSVF

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 .00 RPM 0 .00 RPM
bodymap2_adrenal 0 .00 RPM 0 .08 RPM
bodymap2_brain 0 .00 RPM 0 .00 RPM
bodymap2_breast 0 .00 RPM 0 .04 RPM
bodymap2_colon 0 .08 RPM 0 .00 RPM
bodymap2_heart 0 .06 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .05 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .00 RPM 0 .17 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 0 .06 RPM
bodymap2_thyroid 0 .00 RPM 0 .04 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3553 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3553 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3553 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3553 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3553 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2414
Pongo abelii retro_pabe_2934
Parental genes homology:
Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000113841 retrocopy
retro_cjac_100,
Dipodomys ordii ENSDORG000000050581 retrocopy
retro_dord_340,
Equus caballus ENSECAG000000119081 retrocopy
retro_ecab_575,
Echinops telfairi ENSETEG000000090262 retrocopies
retro_etel_1006, retro_etel_204,
Homo sapiens ENSG00000205126 1 retrocopy
retro_hsap_3553 ,
Myotis lucifugus ENSMLUG000000051511 retrocopy
retro_mluc_1235,
Nomascus leucogenys ENSNLEG000000179661 retrocopy
retro_nleu_2326,
Ochotona princeps ENSOPRG000000020971 retrocopy
retro_opri_526,
Ochotona princeps ENSOPRG000000068057 retrocopies
retro_opri_1064, retro_opri_1151, retro_opri_251, retro_opri_252, retro_opri_398, retro_opri_399, retro_opri_808,
Pongo abelii ENSPPYG000000033401 retrocopy
retro_pabe_2934,
Pan troglodytes ENSPTRG000000286621 retrocopy
retro_ptro_2414,
Tupaia belangeri ENSTBEG000000166231 retrocopy
retro_tbel_3677,
Tursiops truncatus ENSTTRG000000027271 retrocopy
retro_ttru_1321,

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 = 0.07 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 .00 RPM
CEU_NA12751 0 .00 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 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 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 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .07 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 .02 RPM

Indel association:

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



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