RetrogeneDB ID:

retro_hsap_865

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:34356663..34357429(-)
Located in intron of:ENSG00000166016
Retrocopy
information
Ensembl ID:ENSG00000254708
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MMADHC
Ensembl ID:ENSG00000168288
Aliases:MMADHC, C2orf25, CL25022, cblD
Description:methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria [Source:HGNC Symbol;Acc:25221]


Retrocopy-Parental alignment summary:






>retro_hsap_865
TCTCATGTGGCCGCTCTACCTCCAGATATATGCTCTCAAAAGGTGTGGCCTGATGAAACTATGGGACCGTTTGGACCTCA
AGATCAGAGGTTCAAGCTTCCTGGGATCATAGGTTTTGATTGTCACCTCAATGGGACTGCTTCACAGAAGAAAAGCCTGC
TTTATAAAACTTTGCCTGATGTTCTAGCAGAAACTTTATCAAGTGAAAGACACAAGTTTGTGATGACACAATATGTGAAT
GAATTTCAGGGTAATGATGCACCTGTTGAACAAGAAATTAACAGTGCAGAAACTTAACTTTGAAAGTGCCAGAGTGGAGT
GTGCAATACAAACGTGTCCAGAATTGTGGCGAAAAGATTTTGAATCACTGTTTCCAGAAGTAGCTAATAGCAAATTAATC
ATTCTGACTGTAACACAGAAAACTAAGAATAATATGACTGTTTAGAGTGAAGAAGTAGAAACTGAAAGAGAAGTGCTCTT
AGAAAAGTTCATCAATGTTGCTAAGGAAATTTGCTGTACTCTTTGTGCTGAGGGATATTGGGCTGACTTTACTGACCCAT
CATCTGGTTTGGCATTTTTTTGGACCATATACAAACAACAATCTTTTTGAAACTGATGAATGCTACCGACATTTAGGATT
CTCTGTTGATGACCTTCGATGCTTAAAGTGATTCGTCATAGTCTCTGGGGTACCCGTGTAGTTGTAGGAAGCATCTTCAC
TAATGCAACACCAGACAGCCATATTATGAAGAAATTAAGTGGAAAT

ORF - retro_hsap_865 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.37 %
Parental protein coverage: 86.15 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSHVAAAPPDICSRTVWPDETMGPFGPQDQRFQLPGNIGFDCHLNGTASQKKSLVHKTLPDVLAEPLSSER
SHVAA.PPDICS..VWPDETMGPFGPQDQRF.LPG.IGFDCHLNGTASQKKSL..KTLPDVLAE.LSSER
RetrocopySHVAALPPDICSQKVWPDETMGPFGPQDQRFKLPGIIGFDCHLNGTASQKKSLLYKTLPDVLAETLSSER
ParentalHEFVMAQYVNEFQGNDAPVEQEINSAET-YFESARVECAIQTCPELLRKDFESLFPEVANGKLMILTVTQ
H.FVM.QYVNEFQGNDAPVEQEINSAET..FESARVECAIQTCPEL.RKDFESLFPEVAN.KL.ILTVTQ
RetrocopyHKFVMTQYVNEFQGNDAPVEQEINSAET>NFESARVECAIQTCPELWRKDFESLFPEVANSKLIILTVTQ
ParentalKTKNDMTVWSEEVEIEREVLLEKFINGAKEICYALRAEGYWADFIDPSSGLA-FFGPYTNNTLFETDERY
KTKN.MTV.SEEVE.EREVLLEKFIN.AKEIC..L.AEGYWADF.DPSSGLA.FFGPYTNN.LFETDE.Y
RetrocopyKTKNNMTV*SEEVETEREVLLEKFINVAKEICCTLCAEGYWADFTDPSSGLA>FFGPYTNNNLFETDECY
ParentalRHLGFSVDDLGC-CKVIRHSLWGTHVVVGSIFTNATPDSHIMKKLSGN
RHLGFSVDDL.C..KVIRHSLWGT.VVVGSIFTNATPDSHIMKKLSGN
RetrocopyRHLGFSVDDLRC<LKVIRHSLWGTRVVVGSIFTNATPDSHIMKKLSGN

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 60 .65 RPM
bodymap2_adrenal 0 .00 RPM 60 .36 RPM
bodymap2_brain 0 .12 RPM 45 .68 RPM
bodymap2_breast 0 .02 RPM 81 .65 RPM
bodymap2_colon 0 .14 RPM 86 .97 RPM
bodymap2_heart 0 .30 RPM 83 .00 RPM
bodymap2_kidney 0 .00 RPM 85 .95 RPM
bodymap2_liver 0 .00 RPM 85 .68 RPM
bodymap2_lung 0 .02 RPM 55 .47 RPM
bodymap2_lymph_node 0 .15 RPM 65 .40 RPM
bodymap2_ovary 0 .13 RPM 65 .83 RPM
bodymap2_prostate 0 .12 RPM 95 .16 RPM
bodymap2_skeletal_muscle 0 .07 RPM 87 .94 RPM
bodymap2_testis 0 .00 RPM 86 .27 RPM
bodymap2_thyroid 0 .06 RPM 83 .65 RPM
bodymap2_white_blood_cells 0 .00 RPM 82 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_865 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_865 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_13748671 libraries909 libraries244 libraries4 libraries1 library

The graphical summary, for retro_hsap_865 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_865 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_865 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_599
Gorilla gorilla retro_ggor_704
Macaca mulatta retro_mmul_1058
Parental genes homology:
Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000030862 retrocopies
retro_cjac_4082, retro_cjac_4101,
Cavia porcellus ENSCPOG000000076901 retrocopy
retro_cpor_30,
Homo sapiens ENSG00000168288 2 retrocopies
retro_hsap_4716, retro_hsap_865 ,
Gorilla gorilla ENSGGOG000000273481 retrocopy
retro_ggor_704,
Macaca mulatta ENSMMUG000000056331 retrocopy
retro_mmul_1058,
Monodelphis domestica ENSMODG000000035662 retrocopies
retro_mdom_1749, retro_mdom_620,
Mustela putorius furoENSMPUG000000003231 retrocopy
retro_mputfur_1253,
Nomascus leucogenys ENSNLEG000000107952 retrocopies
retro_nleu_1988, retro_nleu_426,
Otolemur garnettii ENSOGAG000000343854 retrocopies
retro_ogar_3266, retro_ogar_356, retro_ogar_688, retro_ogar_813,
Pan troglodytes ENSPTRG000000125251 retrocopy
retro_ptro_599,
Ictidomys tridecemlineatus ENSSTOG000000215761 retrocopy
retro_itri_1809,
Tarsius syrichta ENSTSYG000000090751 retrocopy
retro_tsyr_1690,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 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 .08 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .07 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 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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





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