RetrogeneDB ID:

retro_hsap_3597

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:56296727..56298031(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000220666
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RCC2
Ensembl ID:ENSG00000179051
Aliases:RCC2, TD-60
Description:regulator of chromosome condensation 2 [Source:HGNC Symbol;Acc:30297]


Retrocopy-Parental alignment summary:






>retro_hsap_3597
ACAAGCGCGCGGGGCGCCAAGGAGCGCGTCAAACTTAAAGGGTCAAAGTGCAATGGGCAGCTTTTGATTTTGGGGGCAAC
TAACTGGGACATGATTGGTCGAAAAGAAGTGCCTAAACAGCAAACTGCTTACCGCGATCTCGGTCAGAATTTGTGGGGTC
CCCACAGGTATGGCTGTCTGGCGGGGGTCCGGATACGGACAGTGATCTCAGGTTCCTGTGCTGCACACAGCCTCCTCATC
ACCATGGAAGGGAAGCTGTGGAGTTGGGGTCGAAATGAGAAGGGGCAGCTGGGACATGGCGACACCAAGAGAGTAGAGGC
CCCCAGATTCATCGAGGGTCTCTGCCATGAAGTGACCATGTCTGCAGCATGTGGGTGGAACCACACCTTGGCCTTGACGA
AAACGGGCTCTGTGTTTGCGTTTGGGGAGAACAAGATGGGGCAGCTGGGCCTTGCCAACCAGACAGACGCTGTGCAGCCC
CGCGCGGATAATGTATAACGGCCAGCCAATTACCAAAATGGCCTGTGGGGCTGAATTCAGTATGATAATGGACTGAAAAG
GAAACCTCTATTCCTTTGGGTGCCCTGAATATGGCCAGCTGGGACACAACTCGGATGGGAAGTTCATCTTTGGGGCACGG
CGGATAGAGTACGACTGCGAACTGGTTCCCCCGCGACTGGCCATATTCATTGAGAAGACGAAAGACGGACAGATTCTGCC
TGTACCAAACGTGGTTGTGTGAGACGTGGCCTGTGGTGCTAACCACACGTGGTCCTGGACTCCCAGAAGCGAGTCTTCTC
CTGGGGCTTCGGTGGCTATGGCCGGCTCGGCCACGCAGAGCAGAAGGACGAGATGGTCCGCCGCCTGGTGAAGCTGTTTG
ACTTCCCTTGGCGTGGTGCGTCCCAGATCTATGCTGGTTACACCTGCTCCTTGGCCGTCAGTGAAGTGGGTGGTCTGTTT
TTCCGGAGGGCCACCACTACCTCCCGTGAATCTGCCATGTACCCGAAAGCAGTGCAGGACCTCTGTGGCTGGAGAATCCA
GAGCCTGGCTTGTGGGAAGAGCAGTATCATTGTGGCCGCCGACGAGAGCGCCATCAGCTGGGGCCTATCACCGACCTTCG
GGGAACTGGGCTAGGGGGACCACAAGCCCAAGTCTTCCACTGCAGCCCAGGAGGTGAAGACTCTGCATCCACAGTCTTCA
TTTTCTCAGAGAAGGTCGCCATGGGCTACTCACACTCCTTGGTGATAGCAAGAGACGAAAGTGAGACCGAGAAAGAGATC
AAGAAACTGCCAGAATACAACCCC

ORF - retro_hsap_3597 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.41 %
Parental protein coverage: 83.14 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTEPEHTKERVKLEGSKCKGQLLIFGATNWDLIGRKEVPKQQAAYRNLGQNLWGPHRYGCLAGVRVRTVVS
T.....KERVKL.GSKC.GQLLI.GATNWD.IGRKEVPKQQ.AYR.LGQNLWGPHRYGCLAGVR.RTV.S
RetrocopyTSARGAKERVKLKGSKCNGQLLILGATNWDMIGRKEVPKQQTAYRDLGQNLWGPHRYGCLAGVRIRTVIS
ParentalGSCAAHSLLITTEGKLWSWGRNEKGQLGHGDTKRVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFA
GSCAAHSLLIT.EGKLWSWGRNEKGQLGHGDTKRVEAPR.IEGL.HEV..SAACG.NHTLALT.TGSVFA
RetrocopyGSCAAHSLLITMEGKLWSWGRNEKGQLGHGDTKRVEAPRFIEGLCHEVTMSAACGWNHTLALTKTGSVFA
ParentalF-GENKMGQLGLGNQTDAVPSPAQIMYNGQPITKMACGAEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKF
F.G....G...L........SPA.IMYNGQPITKMACGAEFSMIMD.KGNLYSFGCPEYGQLGHNSDGKF
RetrocopyF>GRTRWGSWALPTR-QTLCSPARIMYNGQPITKMACGAEFSMIMD*KGNLYSFGCPEYGQLGHNSDGKF
ParentalIARAQRIEYDCELVPRRVAIFIEKTKDGQILPVPNVVVRDVACGANHT-LVLDSQKRVFSWGFGGYGRLG
I..A.RIEYDCELVP.R.AIFIEKTKDGQILPVPNVVV.DVACGANHT..VLDSQKRVFSWGFGGYGRLG
RetrocopyIFGARRIEYDCELVPPRLAIFIEKTKDGQILPVPNVVV*DVACGANHT<VVLDSQKRVFSWGFGGYGRLG
ParentalHAEQKDEMVPRLVKLFDFPGRGASQIYAGYTCSFAVSEVGGLFFWGATNTSRESTMYPKAVQDLCGWRIR
HAEQKDEMV.RLVKLFDFP.RGASQIYAGYTCS.AVSEVGGLFF..AT.TSRES.MYPKAVQDLCGWRI.
RetrocopyHAEQKDEMVRRLVKLFDFPWRGASQIYAGYTCSLAVSEVGGLFFRRATTTSRESAMYPKAVQDLCGWRIQ
ParentalSLACGKSSIIVAADESTISWGPSPTFGELGYGDHKPKSSTAAQEVKTL--DGIFSEQVAMGYSHS-LVIA
SLACGKSSIIVAADES.ISWG.SPTFGELG.GDHKPKSSTAAQEVKTL.....FS........H......
RetrocopySLACGKSSIIVAADESAISWGLSPTFGELG*GDHKPKSSTAAQEVKTLHPQSSFSQRRSPWATHT<SLVI
ParentalRDESETEKEKIKKLPEYNP
..........IKKLPEYNP
RetrocopyARDESETEKEIKKLPEYNP

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 .11 RPM
bodymap2_adrenal 0 .00 RPM 85 .62 RPM
bodymap2_brain 0 .00 RPM 17 .13 RPM
bodymap2_breast 0 .00 RPM 48 .89 RPM
bodymap2_colon 0 .00 RPM 37 .09 RPM
bodymap2_heart 0 .00 RPM 13 .98 RPM
bodymap2_kidney 0 .00 RPM 32 .65 RPM
bodymap2_liver 0 .08 RPM 10 .50 RPM
bodymap2_lung 0 .00 RPM 56 .82 RPM
bodymap2_lymph_node 0 .00 RPM 97 .87 RPM
bodymap2_ovary 0 .00 RPM 76 .93 RPM
bodymap2_prostate 0 .00 RPM 45 .29 RPM
bodymap2_skeletal_muscle 0 .00 RPM 12 .88 RPM
bodymap2_testis 0 .02 RPM 65 .95 RPM
bodymap2_thyroid 0 .00 RPM 40 .26 RPM
bodymap2_white_blood_cells 0 .00 RPM 116 .24 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3597 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3597 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3597 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3597 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3597 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2434
Pongo abelii retro_pabe_2957
Parental genes homology:
Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000013961 retrocopy
retro_dnov_2692,
Homo sapiens ENSG00000179051 3 retrocopies
retro_hsap_2677, retro_hsap_3073, retro_hsap_3597 ,
Gorilla gorilla ENSGGOG000000152631 retrocopy
retro_ggor_2112,
Nomascus leucogenys ENSNLEG000000077832 retrocopies
retro_nleu_2483, retro_nleu_298,
Otolemur garnettii ENSOGAG000000145441 retrocopy
retro_ogar_2967,
Pongo abelii ENSPPYG000000258343 retrocopies
retro_pabe_2547, retro_pabe_2957, retro_pabe_748,
Pan troglodytes ENSPTRG000000002473 retrocopies
retro_ptro_1804, retro_ptro_2072, retro_ptro_2434,
Rattus norvegicus ENSRNOG000000063271 retrocopy
retro_rnor_1378,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 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 .03 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 .04 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 .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).



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