RetrogeneDB ID:

retro_hsap_2501

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:21:27064537..27064863(+)
Located in intron of:ENSG00000154721
Retrocopy
information
Ensembl ID:ENSG00000227054
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FDX1
Ensembl ID:ENSG00000137714
Aliases:FDX1, ADX, FDX, LOH11CR1D
Description:ferredoxin 1 [Source:HGNC Symbol;Acc:3638]


Retrocopy-Parental alignment summary:






>retro_hsap_2501
AACAGTGAAACATTAACAAACAAAGGAAAAGTTGATGACTCTTTGCTAGATGTTGTGGTTGAAAATAATGTAGATATTGA
TGGGTTTGTTGCATGGCAGGGAACCTTGGCTTGCTCTGTCACCTCATTTTTGAAAAGCACATATTTGAGAAGTTAGACAC
AATCACTGACAAGGAGATTGACATGCTTGATCTGGCATATGGACTGACAGACAGGTCAGAGTTGTATTGCCAAATCTGTT
TGACAAAATCTATGGGCCATATGACTGTCTGAGTACCTGATGGAGTGGCCAGTGCCAGACAATCCACTGATATGGGCAAG
ACCACC

ORF - retro_hsap_2501 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.97 %
Parental protein coverage: 59.78 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDGETLTTKGKVGDSLLDVVVENNLDIDGFGACE-GTLACSTCHLIFEDHIYEKLDAITDEENDMLDLAYG
..ETLT.KGKV.DSLLDVVVENN.DIDGF.A...G.L....CHLIFE.HI.EKLD.ITD.E.DMLDLAYG
RetrocopyNSETLTNKGKVDDSLLDVVVENNVDIDGFVAWQ<GNLGL-LCHLIFEKHIFEKLDTITDKEIDMLDLAYG
ParentalLTDRSRLGCQICLTKSMDNMTVRVPETVADARQSIDVGKTS
LTDRS.L.CQICLTKSM..MTV.VP..VA.ARQS.D.GKT.
RetrocopyLTDRSELYCQICLTKSMGHMTV*VPDGVASARQSTDMGKTT

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 22 .30 RPM
bodymap2_adrenal 0 .00 RPM 31 .34 RPM
bodymap2_brain 0 .02 RPM 26 .14 RPM
bodymap2_breast 0 .00 RPM 38 .09 RPM
bodymap2_colon 0 .10 RPM 31 .23 RPM
bodymap2_heart 0 .00 RPM 33 .10 RPM
bodymap2_kidney 0 .00 RPM 64 .05 RPM
bodymap2_liver 0 .00 RPM 72 .52 RPM
bodymap2_lung 0 .00 RPM 39 .50 RPM
bodymap2_lymph_node 0 .00 RPM 23 .19 RPM
bodymap2_ovary 0 .00 RPM 34 .89 RPM
bodymap2_prostate 0 .00 RPM 39 .49 RPM
bodymap2_skeletal_muscle 0 .00 RPM 27 .74 RPM
bodymap2_testis 0 .06 RPM 34 .60 RPM
bodymap2_thyroid 0 .08 RPM 74 .53 RPM
bodymap2_white_blood_cells 0 .00 RPM 27 .84 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2501 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2501 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2501 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2501 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2501 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1560
Pan troglodytes retro_ptro_1452
Pongo abelii retro_pabe_1841
Callithrix jacchus retro_cjac_2028
Parental genes homology:
Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000103951 retrocopy
retro_cjac_2028,
Homo sapiens ENSG00000137714 2 retrocopies
retro_hsap_2472, retro_hsap_2501 ,
Homo sapiens ENSG000002676731 retrocopy
retro_hsap_331,
Gorilla gorilla ENSGGOG000000224431 retrocopy
retro_ggor_1560,
Nomascus leucogenys ENSNLEG000000072491 retrocopy
retro_nleu_1432,
Oryctolagus cuniculus ENSOCUG000000178261 retrocopy
retro_ocun_1907,
Pongo abelii ENSPPYG000000038532 retrocopies
retro_pabe_1822, retro_pabe_1841,
Pan troglodytes ENSPTRG000000042602 retrocopies
retro_ptro_1428, retro_ptro_1452,

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 = 0.03 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 .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 .03 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).



Copyright © RetrogeneDB 2014-2017