RetrogeneDB ID:

retro_hsap_1373

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:93604442..93604809(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000258595
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CYB5A
Ensembl ID:ENSG00000166347
Aliases:CYB5A, CYB5, MCB5
Description:cytochrome b5 type A (microsomal) [Source:HGNC Symbol;Acc:2570]


Retrocopy-Parental alignment summary:






>retro_hsap_1373
GCCGAGCAGCTGGACGAGGCCGTGAAGTACTACACCCTAGAGGAGATTCAGAAGCACAACGACAGCAAGAGCACCTGACT
GATTCTGCACCACAAGTGTACTATTTGACCAAATTTCTGGAAGAGCATTCTGGTGGGGAAGAAGTCTTAAGGGAACAAGC
TGGAGGTGACGCTACTGAGAATTTTGAGGATGTCGGGCATCTTTGAGATGCCATGGAATTGTCCAAAACATATATCATTC
AGGAGCCCCATCCAGACGACAGACCAAAGTTAAACAAGCTTCGGAAACTCTTATCACTGCTGTTGATTCTAGCTCCAGTT
GGTGGACCAACTGAGTGATCCCTGCCATGTCAGCAGTGGCCGTCGCC

ORF - retro_hsap_1373 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84. %
Parental protein coverage: 91.79 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAEQSDEAVKYYTLEEIQKHNHSKSTWLILHHK-VYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHST
AEQ.DEAVKYYTLEEIQKHN.SKST.LILHHK.VY.LTKFLEEH.GGEEVLREQAGGDATENFEDVGH..
RetrocopyAEQLDEAVKYYTLEEIQKHNDSKST*LILHHK<VYYLTKFLEEHSGGEEVLREQAGGDATENFEDVGHL*
ParentalDAREMSKTFIIGELHPDDRPKLNK-PPETLITTIDSSSSWWTNWVIPAISAVAVA
DA.E.SKT.II.E.HPDDRPKLNK...ETLIT..DSSSSWWTN.VIPA.SAVAVA
RetrocopyDAMELSKTYIIQEPHPDDRPKLNK<ASETLITAVDSSSSWWTN*VIPAMSAVAVA

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 68 .12 RPM
bodymap2_adrenal 0 .00 RPM 29 .11 RPM
bodymap2_brain 0 .00 RPM 15 .78 RPM
bodymap2_breast 0 .00 RPM 125 .02 RPM
bodymap2_colon 0 .00 RPM 74 .54 RPM
bodymap2_heart 0 .00 RPM 21 .51 RPM
bodymap2_kidney 0 .00 RPM 218 .84 RPM
bodymap2_liver 0 .00 RPM 640 .01 RPM
bodymap2_lung 0 .00 RPM 152 .64 RPM
bodymap2_lymph_node 0 .00 RPM 43 .27 RPM
bodymap2_ovary 0 .00 RPM 122 .33 RPM
bodymap2_prostate 0 .00 RPM 116 .51 RPM
bodymap2_skeletal_muscle 0 .00 RPM 4 .15 RPM
bodymap2_testis 0 .00 RPM 39 .74 RPM
bodymap2_thyroid 0 .00 RPM 23 .35 RPM
bodymap2_white_blood_cells 0 .00 RPM 7 .19 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1373 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1373 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_416011497 libraries251 libraries72 libraries7 libraries2 libraries

The graphical summary, for retro_hsap_1373 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1373 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1373 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1068
Pongo abelii retro_pabe_1140
Parental genes homology:
Parental genes homology involve 27 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136142 retrocopies
retro_amel_1727, retro_amel_860,
Canis familiaris ENSCAFG000000000262 retrocopies
retro_cfam_32, retro_cfam_787,
Choloepus hoffmanni ENSCHOG000000003592 retrocopies
retro_chof_128, retro_chof_239,
Callithrix jacchus ENSCJAG000000031633 retrocopies
retro_cjac_2427, retro_cjac_2602, retro_cjac_686,
Cavia porcellus ENSCPOG000000121111 retrocopy
retro_cpor_1140,
Equus caballus ENSECAG000000175811 retrocopy
retro_ecab_12,
Erinaceus europaeus ENSEEUG000000106831 retrocopy
retro_eeur_587,
Echinops telfairi ENSETEG000000006911 retrocopy
retro_etel_381,
Homo sapiens ENSG000001030181 retrocopy
retro_hsap_1493,
Homo sapiens ENSG00000166347 3 retrocopies
retro_hsap_1307, retro_hsap_1373 , retro_hsap_2462,
Gorilla gorilla ENSGGOG000000079681 retrocopy
retro_ggor_1068,
Macropus eugenii ENSMEUG000000158991 retrocopy
retro_meug_1573,
Myotis lucifugus ENSMLUG000000114625 retrocopies
retro_mluc_1159, retro_mluc_1333, retro_mluc_1475, retro_mluc_1701, retro_mluc_1908,
Macaca mulatta ENSMMUG000000136073 retrocopies
retro_mmul_2162, retro_mmul_2199, retro_mmul_546,
Mustela putorius furoENSMPUG000000166301 retrocopy
retro_mputfur_776,
Mus musculus ENSMUSG000000246461 retrocopy
retro_mmus_2177,
Nomascus leucogenys ENSNLEG000000092321 retrocopy
retro_nleu_1066,
Otolemur garnettii ENSOGAG000000000524 retrocopies
retro_ogar_1248, retro_ogar_1888, retro_ogar_2041, retro_ogar_2869,
Ochotona princeps ENSOPRG000000115843 retrocopies
retro_opri_1091, retro_opri_296, retro_opri_405,
Pongo abelii ENSPPYG000000092402 retrocopies
retro_pabe_1094, retro_pabe_1140,
Pan troglodytes ENSPTRG000000101113 retrocopies
retro_ptro_1421, retro_ptro_898, retro_ptro_943,
Rattus norvegicus ENSRNOG000000152052 retrocopies
retro_rnor_1565, retro_rnor_2455,
Ictidomys tridecemlineatus ENSSTOG000000224361 retrocopy
retro_itri_1617,
Tupaia belangeri ENSTBEG000000149983 retrocopies
retro_tbel_3229, retro_tbel_3338, retro_tbel_4600,
Tarsius syrichta ENSTSYG000000022411 retrocopy
retro_tsyr_1033,
Tursiops truncatus ENSTTRG000000152721 retrocopy
retro_ttru_1588,
Drosophila melanogaster FBgn00298541 retrocopy
retro_dmel_39,

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 .03 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 .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 .02 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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