RetrogeneDB ID:

retro_hsap_44

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:140682526..140683432(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000120329
Aliases:SLC25A2, ORC2, ORNT2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A15
Ensembl ID:ENSG00000102743
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15 [Source:HGNC Symbol;Acc:10985]


Retrocopy-Parental alignment summary:






>retro_hsap_44
ATGAAGTCCGGTCCTGGCATCCAAGCCGCCATCGACCTCACAGCGGGGGCCGCAGGGGGGACAGCGTGTGTACTGACTGG
GCAGCCCTTCGACACAATAAAAGTGAAGATGCAGACGTTCCCTGACCTGTACAAGGGCCTCACCGACTGCTTCCTGAAGA
CATACGCCCAAGTGGGTCTCCGGGGCTTCTACAAGGGCACCGGCCCGGCACTTATGGCCTACGTCGCCGAAAACTCGGTC
CTCTTCATGTGCTACGGGTTCTGCCAGCAGTTTGTCAGGAAAGTGGCTGGAATGGACAAGCAGGCAAAGCTGAGTGATCT
CCAGACTGCAGCCGCGGGGTCCTTCGCCTCTGCATTTGCTGCACTGGCTCTCTGCCCCACTGAGCTTGTGAAGTGCCGGC
TACAGACCATGTATGAAATGGAGATGTCAGGGAAGATAGCAAAAAGCCATAATACAATTTGGTCTGTCGTGAAGGGTATC
CTTAAAAAGGATGGCCCCTTGGGCTTCTACCATGGACTCTCGAGTACTCTACTTCAAGAAGTACCGGGTTATTTCTTTTT
CTTTGGTGGCTATGAACTGAGCCGATCGTTTTTTGCGTCAGGGAGATCAAAAGATGAACTAGGCCCTGTCCATTTGATGT
TAAGTGGTGGAGTTGCTGGAATTTGCCTGTGGCTTGTCGTGTTCCCAGTGGATTGTATTAAATCCAGAATTCAAGTTCTT
TCCATGTATGGGAAACAGGCAGGATTTATTGGTACCCTCTTAAGTGTTGTGAGAAATGAAGGAATAGTAGCCTTATATTC
TGGACTGAAAGCTACTATGATTCGAGCAATCCCTGCCAATGGGGCACTGTTTGTGGCCTACGAATACAGCAGGAAGATGA
TGATGAAACAGTTGGAAGCATACTGA

ORF - retro_hsap_44 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.38 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKSNPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA
MKS.P.IQAAIDLTAGAAGGTACVLTGQPFDT.KVKMQTFPDLY.GLTDC.LKTY.QVG.RGFYKGT.PA
RetrocopyMKSGPGIQAAIDLTAGAAGGTACVLTGQPFDTIKVKMQTFPDLYKGLTDCFLKTYAQVGLRGFYKGTGPA
ParentalLIANIAENSVLFMCYGFCQQVVRKVAGLDKQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEM
L.A..AENSVLFMCYGFCQQ.VRKVAG.DKQAKLSDLQ.AAAGSFASAFAAL.LCPTELVKCRLQTMYEM
RetrocopyLMAYVAENSVLFMCYGFCQQFVRKVAGMDKQAKLSDLQTAAAGSFASAFAALALCPTELVKCRLQTMYEM
ParentalETSGKIAKSQNTVWSVIKSILRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPV
E.SGKIAKS.NT.WSV.K.IL.KDGPLGFYHGLSSTLL.EVPGYFFFFGGYELSRSFFASGRSKDELGPV
RetrocopyEMSGKIAKSHNTIWSVVKGILKKDGPLGFYHGLSSTLLQEVPGYFFFFGGYELSRSFFASGRSKDELGPV
ParentalPLMLSGGVGGICLWLAVYPVDCIKSRIQVLSMSGKQAGFIRTFINVVKNEGITALYSGLKPTMIRAFPAN
.LMLSGGV.GICLWL.V.PVDCIKSRIQVLSM.GKQAGFI.T...VV.NEGI.ALYSGLK.TMIRA.PAN
RetrocopyHLMLSGGVAGICLWLVVFPVDCIKSRIQVLSMYGKQAGFIGTLLSVVRNEGIVALYSGLKATMIRAIPAN
ParentalGALFLAYEYSRKLMMNQLEAY
GALF.AYEYSRK.MM.QLEAY
RetrocopyGALFVAYEYSRKMMMKQLEAY

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 2 .31 RPM
bodymap2_adrenal 0 .31 RPM 3 .81 RPM
bodymap2_brain 0 .00 RPM 2 .09 RPM
bodymap2_breast 0 .02 RPM 2 .94 RPM
bodymap2_colon 0 .00 RPM 1 .57 RPM
bodymap2_heart 0 .00 RPM 2 .53 RPM
bodymap2_kidney 0 .00 RPM 7 .28 RPM
bodymap2_liver 0 .00 RPM 59 .63 RPM
bodymap2_lung 0 .00 RPM 1 .21 RPM
bodymap2_lymph_node 0 .00 RPM 2 .10 RPM
bodymap2_ovary 0 .00 RPM 6 .73 RPM
bodymap2_prostate 0 .00 RPM 2 .08 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .89 RPM
bodymap2_testis 3 .70 RPM 11 .12 RPM
bodymap2_thyroid 0 .00 RPM 5 .95 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .02 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_44 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_44 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_1496651823 libraries3 libraries3 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_44 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_44 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_44 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2303
Gorilla gorilla retro_ggor_2294
Pongo abelii retro_pabe_82
Parental genes homology:
Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000177971 retrocopy
retro_cjac_1776,
Cavia porcellus ENSCPOG000000055702 retrocopies
retro_cpor_105, retro_cpor_107,
Equus caballus ENSECAG000000076661 retrocopy
retro_ecab_72,
Homo sapiens ENSG00000102743 1 retrocopy
retro_hsap_44 ,
Gorilla gorilla ENSGGOG000000252611 retrocopy
retro_ggor_2294,
Microcebus murinus ENSMICG000000072181 retrocopy
retro_mmur_18,
Macaca mulatta ENSMMUG000000225851 retrocopy
retro_mmul_199,
Nomascus leucogenys ENSNLEG000000011851 retrocopy
retro_nleu_1704,
Otolemur garnettii ENSOGAG000000093801 retrocopy
retro_ogar_490,
Pongo abelii ENSPPYG000000053071 retrocopy
retro_pabe_82,
Pan troglodytes ENSPTRG000000058091 retrocopy
retro_ptro_2303,
Pteropus vampyrus ENSPVAG000000103931 retrocopy
retro_pvam_15,
Ictidomys tridecemlineatus ENSSTOG000000078401 retrocopy
retro_itri_726,
Tupaia belangeri ENSTBEG000000172391 retrocopy
retro_tbel_4583,

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 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 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 .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 .05 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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