RetrogeneDB ID:

retro_hsap_2631

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:34914216..34915192(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235534
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FECH
Ensembl ID:ENSG00000066926
Aliases:None
Description:ferrochelatase [Source:HGNC Symbol;Acc:3647]


Retrocopy-Parental alignment summary:






>retro_hsap_2631
ACAGAAACAGCCCAGTGTGGCCAGGGTGCAAAACCTCAAGTTCAAGTGAAGAGGAAGCTGAAAACTGGAATATTAATGCT
AAACATGGGAGGACCTGAAACCCTCTGACACGTTCATGACTTCCTTCTGAGGCTCTTTTTGGACCAAGACCTCATGACAC
TTACTGTTCAAAATAAGTTTACACCATTCTTTGCCAAATGCAGAACCTCCAAGATTCAAGGGCAGTACCACAGAACAGGA
GGTGGGTCCTCCATCAAGATGTGGATTTCCAAGCAGGGAGAAGGTATTATGGTGAAGCTGCTGGATGACTTGTCCCCCTA
CACAGCCCCTCACAAATAATACTTCATTGGATTTTGGCATGTCCATTCTTTACTAAAAGAAGCAAATGAAGAGATGGAGA
GAGATGGCCTGGAAAGGGCTATTGCTTTCATGCAGGATCCACAGTATGCTTGCTGTACCACAGGCGGCAGCTTAAATGCC
ATTTAAAGATCCTATAATAGAGTGGGACAGAAGTTTACAATGAAGTGCAGCACTATCAGTAGGTGGCCCACCCATTGCCT
CCTCACCCACTGCTTTGTTGACTACATTCTGAAAGAGCTGGACCATTTTCCACTGGAGAAGAGAAGCGAGTCGGCCATTC
TCTTTTCTGCTCACTCACTGCCAATATCCGTGATCAACAGAGGAGACCCCTATTCTCAGGAGTTAAGTGCCACTATCCAA
AAAGTCATAGAAAGGTTGGGTTACTGCAACCCTTACCAGCTGGTGTGAGGATCCAAGGTTGGTTCAGTGCCCTGGATGGG
TCTTCAAACAGATGAAATCTATCAGAGGGCTTTCTGAGAGGGGAAAGAAGAATATCCTCTCACTTTTGATAGCATTTACC
AACGATAACACCGAAATGCTGTAGAAACTGGATATCGAGTACGCTCAAGTTTTAGACAATGAGTGTGGAGTTGAAAACAT
CAGAAGAGCAGCCTCT

ORF - retro_hsap_2631 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.92 %
Parental protein coverage: 76.6 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTETAQHAQGAKPQVQPQKRKPKTGILMLNMGGPETLGDVHDFLLRLFLDRDLMTLPIQNKLAPFIAKRRT
TETAQ..QGAKPQVQ..KRK.KTGILMLNMGGPETL..VHDFLLRLFLD.DLMTL..QNK..PF.AK.RT
RetrocopyTETAQCGQGAKPQVQV-KRKLKTGILMLNMGGPETL*HVHDFLLRLFLDQDLMTLTVQNKFTPFFAKCRT
ParentalPKIQEQYRRIGGGSPIKIWTSKQGEG-MVKLLDELSPNTAPHK-YYIGFRYVHPLTEEAIEEMERDGLER
.KIQ.QY.R.GGGS.IK.W.SKQGEG.MVKLLD.LSP.TAPHK.Y.IGF..VH.L..EA.EEMERDGLER
RetrocopySKIQGQYHRTGGGSSIKMWISKQGEGIMVKLLDDLSPYTAPHK*YFIGFWHVHSLLKEANEEMERDGLER
ParentalAIAFTQYPQYSCSTTGSSLNAIYRYYNQVGRKPTMKWSTIDRWPTHHLLIQCFADHILKELDHFPLEKRS
AIAF.Q.PQY.C.TTG.SLNAI.R.YN.VG.K.TMK.STI.RWPTH.LL..CF.D.ILKELDHFPLEKRS
RetrocopyAIAFMQDPQYACCTTGGSLNAI*RSYNRVGQKFTMKCSTISRWPTHCLLTHCFVDYILKELDHFPLEKRS
ParentalEVVILFSAHSLPMSVVNRGDPYPQEVSATVQKVMERLEYCNPYRLVWQSKVGPMPWLGPQTDE-SIKGLC
E..ILFSAHSLP.SV.NRGDPY.QE.SAT.QKV.ERL.YCNPY.LV..SKVG..PW.G.QTDE.SI.GL.
RetrocopyESAILFSAHSLPISVINRGDPYSQELSATIQKVIERLGYCNPYQLV*GSKVGSVPWMGLQTDE>SIRGLS
ParentalERGRKNILLVPIAFTSDHIETLYELDIEYSQVLAKECGVENIRRAES
ERG.KNIL...IAFT.D..E.L..LDIEY.QVL..ECGVENIRRA.S
RetrocopyERGKKNILSLLIAFTNDNTEML*KLDIEYAQVLDNECGVENIRRAAS

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 18 .76 RPM
bodymap2_adrenal 0 .00 RPM 23 .03 RPM
bodymap2_brain 0 .00 RPM 31 .18 RPM
bodymap2_breast 0 .00 RPM 25 .95 RPM
bodymap2_colon 0 .00 RPM 13 .42 RPM
bodymap2_heart 0 .00 RPM 25 .79 RPM
bodymap2_kidney 0 .00 RPM 53 .03 RPM
bodymap2_liver 0 .00 RPM 32 .80 RPM
bodymap2_lung 0 .00 RPM 20 .29 RPM
bodymap2_lymph_node 0 .00 RPM 9 .17 RPM
bodymap2_ovary 0 .00 RPM 28 .36 RPM
bodymap2_prostate 0 .00 RPM 29 .06 RPM
bodymap2_skeletal_muscle 0 .00 RPM 23 .99 RPM
bodymap2_testis 0 .00 RPM 19 .21 RPM
bodymap2_thyroid 0 .00 RPM 51 .01 RPM
bodymap2_white_blood_cells 0 .00 RPM 23 .84 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2631 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2631 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2631 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2631 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2631 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1776
Gorilla gorilla retro_ggor_1841
Pongo abelii retro_pabe_2332
Macaca mulatta retro_mmul_1485
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000038731 retrocopy
retro_cjac_4008,
Homo sapiens ENSG00000066926 1 retrocopy
retro_hsap_2631 ,
Gorilla gorilla ENSGGOG000000055541 retrocopy
retro_ggor_1841,
Macaca mulatta ENSMMUG000000225681 retrocopy
retro_mmul_1485,
Nomascus leucogenys ENSNLEG000000080621 retrocopy
retro_nleu_643,
Oryctolagus cuniculus ENSOCUG000000030201 retrocopy
retro_ocun_497,
Pongo abelii ENSPPYG000000091821 retrocopy
retro_pabe_2332,
Pan troglodytes ENSPTRG000000100451 retrocopy
retro_ptro_1776,

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 = 0.02 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 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 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 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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).



Copyright © RetrogeneDB 2014-2017