RetrogeneDB ID:

retro_hsap_1041

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:92924510..92925095(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000258262
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MTCH2
Ensembl ID:ENSG00000109919
Aliases:MTCH2, MIMP, SLC25A50
Description:mitochondrial carrier 2 [Source:HGNC Symbol;Acc:17587]


Retrocopy-Parental alignment summary:






>retro_hsap_1041
GGACCTGGAAATGTGCATAAGGAAGTCTCATCTTCCTTTGACTGAGTTATCAAGGAGACAGCTTGAGAGATGATGGCTCA
TTCTGCTGCTATCCTCATCACATATCCCTTCCATGTGATCACTCTGAGACCTGTGGTACAATTCATTGGCAGAGGACCTA
AGTACTGTGGACTTTGTGACTTCATGACCATCTATCAGAAAGAGGGCATCCTAGGGTTTTTCCCAGGACTGGTTCCTCAC
CTCCTAGGTGACATCATTTCTTTGCGGCTGTGTAGCTCACTGGCCTACCTCATCAATACCTATGCACTGGACAGCAGGGT
TTCTACCATGAATGAAATAGAGTTATTCTCAAGCTGTCACAAGATTTTTGCTGGCATGTTGACCTGTCCCTTTGTGCTTG
TCTCTAATCTTATGGCTGTCAACAACTGTGGTTTTGCTGGTGGATGCCCTCTTTACTCCCCAATGTATACTGCATGGATA
GATTGTTGATGCATGCTACAAAAGCAGGGAAATATAAGCCCAGGAAATAGCTTGTTTTTCCAGAAGTTCCTCTTAAGGAA
GACTTATTCGTGTGATTTGAAGATG

ORF - retro_hsap_1041 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.62 %
Parental protein coverage: 65.02 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGPGNVQKEVSSSFDHVIKETTREMIARSAATLITHPFHVITLRSMVQFIGRESKYCGLCDSIITIYREEG
GPGNV.KEVSSSFD.VIKET..EM.A.SAA.LIT.PFHVITLR..VQFIGR..KYCGLCD...TIY..EG
RetrocopyGPGNVHKEVSSSFD*VIKETA*EMMAHSAAILITYPFHVITLRPVVQFIGRGPKYCGLCD-FMTIYQKEG
ParentalILGFFAGLVPRLLGDILSLWLCNSLAYLVNTYALDSGVSTMNEMKSYSQAVTGFFASMLTYPFVLVSNLM
ILGFF.GLVP.LLGDI.SL.LC.SLAYL.NTYALDS.VSTMNE....S......FA.MLT.PFVLVSNLM
RetrocopyILGFFPGLVPHLLGDIISLRLCSSLAYLINTYALDSRVSTMNEIELFS-SCHKIFAGMLTCPFVLVSNLM
ParentalAVNNCGLAGGCPPYSPIYTSWIDCWCMLQKEGNMSRGNSLFFRKVPFGKTYCCDLKM
AVNNCG.AGGCP.YSP.YT.WIDC.CMLQK.GN.S.GNSLFF.K....KTY.CDLKM
RetrocopyAVNNCGFAGGCPLYSPMYTAWIDC*CMLQKQGNISPGNSLFFQKFLLRKTYSCDLKM

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 42 .28 RPM
bodymap2_adrenal 0 .00 RPM 48 .86 RPM
bodymap2_brain 0 .00 RPM 63 .01 RPM
bodymap2_breast 0 .00 RPM 93 .58 RPM
bodymap2_colon 0 .00 RPM 30 .07 RPM
bodymap2_heart 0 .00 RPM 54 .29 RPM
bodymap2_kidney 0 .00 RPM 123 .38 RPM
bodymap2_liver 0 .00 RPM 168 .16 RPM
bodymap2_lung 0 .00 RPM 23 .84 RPM
bodymap2_lymph_node 0 .00 RPM 26 .15 RPM
bodymap2_ovary 0 .00 RPM 54 .28 RPM
bodymap2_prostate 0 .00 RPM 37 .83 RPM
bodymap2_skeletal_muscle 0 .00 RPM 70 .53 RPM
bodymap2_testis 0 .00 RPM 122 .02 RPM
bodymap2_thyroid 0 .00 RPM 70 .03 RPM
bodymap2_white_blood_cells 0 .00 RPM 45 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1041 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1041 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1041 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1041 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1041 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_710
Gorilla gorilla retro_ggor_822
Pongo abelii retro_pabe_872
Parental genes homology:
Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000187421 retrocopy
retro_btau_1321,
Choloepus hoffmanni ENSCHOG000000084731 retrocopy
retro_chof_2162,
Callithrix jacchus ENSCJAG000000202133 retrocopies
retro_cjac_1551, retro_cjac_2003, retro_cjac_3812,
Dasypus novemcinctus ENSDNOG000000012211 retrocopy
retro_dnov_1867,
Homo sapiens ENSG00000109919 2 retrocopies
retro_hsap_1041 , retro_hsap_1690,
Homo sapiens ENSG000001374092 retrocopies
retro_hsap_3671, retro_hsap_856,
Gorilla gorilla ENSGGOG000000082813 retrocopies
retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Mustela putorius furoENSMPUG000000038521 retrocopy
retro_mputfur_312,
Mus musculus ENSMUSG000000272821 retrocopy
retro_mmus_2657,
Nomascus leucogenys ENSNLEG000000147042 retrocopies
retro_nleu_1335, retro_nleu_913,
Oryctolagus cuniculus ENSOCUG000000063682 retrocopies
retro_ocun_1197, retro_ocun_983,
Otolemur garnettii ENSOGAG000000116071 retrocopy
retro_ogar_2578,
Pongo abelii ENSPPYG000000032963 retrocopies
retro_pabe_1392, retro_pabe_1894, retro_pabe_872,
Pan troglodytes ENSPTRG000000035732 retrocopies
retro_ptro_1144, retro_ptro_710,
Pteropus vampyrus ENSPVAG000000073481 retrocopy
retro_pvam_954,
Sorex araneus ENSSARG000000013991 retrocopy
retro_sara_705,
Sus scrofa ENSSSCG000000132323 retrocopies
retro_sscr_262, retro_sscr_279, retro_sscr_602,
Tursiops truncatus ENSTTRG000000141692 retrocopies
retro_ttru_1476, retro_ttru_353,

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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .06 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 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .08 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 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 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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