RetrogeneDB ID:

retro_hsap_272

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:184535937..184536991(+)
Located in intron of:ENSG00000116667
Retrocopy
information
Ensembl ID:ENSG00000232036
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TRMT2B
Ensembl ID:ENSG00000188917
Aliases:TRMT2B, CXorf34, dJ341D10.3
Description:tRNA methyltransferase 2 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25748]


Retrocopy-Parental alignment summary:






>retro_hsap_272
GCTCAAGGTGAAATTTTACAAAGACTAGAGTCTCACATCCAAATGCTCGATGGAGTCAATGTGACAACAGCTGCACCCAA
ATCTGAGGGGCTGTATTGTCTTCTCCATCCTATAATACCATCTCCTGTCATCAGCAGCTACAGAAATAAGTCCACCTTCT
CTGTGAATCAGGGTCCAGATGGCAATCCAAAGACTGTGGAATATAACCTGGGAACTTGAAGAGACGGGAACATTGTCTGT
GTACAGTCTAACCATCTGAAAAACATCCTTGAGAAAGACAGTCAGGTGGCACAGTACTATGAAGTATTCCTTCCACAGTC
TCCAACAGAGCCCTGCCTTCTTCATGAAGGTGGTTACTGGTGTGAGCTCACAGTCCACACCAATAGCCTAAGGCACACAA
TGGCTGTCATCACATTCCATCCCCAGGAATTAAGTCCAGAGGAGCTCCATGTTCAGAAGGAGACTGTAAAGGAATTTTTC
ATTAAAGGTCCTGGAGCAGTCTGTGACTTGACTTCACCTGACTTCCAGGAAAGCAGGACCTGTTTCAGCCATCATCAGTC
CACCTACCAGCTCTTGTTTGGGGAACCTCATATCTTTAAAGATCTCCTGGGCTTGAAGGTCTGCATCTCTCCAGATGCCT
TTTTCCAGATTAACACTGCTGGTGCAGAGATGCTGTATTGGATTGTAGGGAAGCTGAGTGCAGTGAACTCTAACACCATC
CTCCTTGACATCTGCTGTGGAACCGGTGTGATCAGCCTCCCTCTGGATCAGCTACATCGCAGGTCCTTGGGATTTCGTTG
GTGGGGCAGGCAGTGGAGGATGCTAGGCAGACTGCAGCCTACAATGGCATCACCAGCTTTGAGTTTCATACTGGTCAAGC
AGAGATTTTTCCAGGGCTGCTAAAGTCAAAGGAATATGGACAGTTAATTGTTGCTATGTGAACCCAGCCCATGCTGAACT
GCATTACAAGGAAGTTCAAGCCATTTGAAACTTCAAGGCCCTCCGCATACTAGCTTTTGTTTCCTGCAAGCCCCGTGATG
AAACCACAAGGAAT

ORF - retro_hsap_272 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.91 %
Parental protein coverage: 70.44 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAQKKILQRLESYIQMLNGVSVTTAVPKSERLSCLLHPIIPSPVINGYRNKSTFSVNRGPDGNPKTVGFYL
AQ..ILQRLES.IQML.GV.VTTA.PKSE.L.CLLHPIIPSPVI..YRNKSTFSVN.GPDGNPKTV...L
RetrocopyAQGEILQRLESHIQMLDGVNVTTAAPKSEGLYCLLHPIIPSPVISSYRNKSTFSVNQGPDGNPKTVEYNL
ParentalGTWRDGNVVCVQSNHLKNIPEKHSQVAQYYEVFLRQSPLEPCLVFHEGGYWRELTVRTNSQGHTMAIITF
GT.RDGN.VCVQSNHLKNI.EK.SQVAQYYEVFL.QSP.EPCL..HEGGYW.ELTV.TNS..HTMA.ITF
RetrocopyGT*RDGNIVCVQSNHLKNILEKDSQVAQYYEVFLPQSPTEPCLL-HEGGYWCELTVHTNSLRHTMAVITF
ParentalHPQKLSQEELHVQKEIVKEFFIRGPGAACGLTSLYFQESTMTRCSHQQSPYQLLFGEPYIFEELLSLKIR
HPQ.LS.EELHVQKE.VKEFFI.GPGA.C.LTS..FQES..T..SH.QS.YQLLFGEP.IF..LL.LK..
RetrocopyHPQELSPEELHVQKETVKEFFIKGPGAVCDLTSPDFQES-RTCFSHHQSTYQLLFGEPHIFKDLLGLKVC
ParentalISPDAFFQINTAGAEMLYRTVGELTGVNSDTILLDICCGTGVIGLSLAQ-HTSRVLGIELLEQAVEDARW
ISPDAFFQINTAGAEMLY..VG.L..VNS.TILLDICCGTGVI.L.L.Q..TS.VLGI.L..QAVEDAR.
RetrocopyISPDAFFQINTAGAEMLYWIVGKLSAVNSNTILLDICCGTGVISLPLDQ<ATSQVLGISLVGQAVEDARQ
ParentalTAAFNGITNSEFHTGQAEKILPGLLKSKEDGQSIVAV-VNPARAGLHYKVIQAIRNFRAIHTLVFVSCKL
TAA.NGIT..EFHTGQAE.I.PGLLKSKE.GQ.IVA..VNPA.A.LHYK..QAI.NF.A...L.FVSCK.
RetrocopyTAAYNGITSFEFHTGQAE-IFPGLLKSKEYGQLIVAM<VNPAHAELHYKEVQAI*NFKALRILAFVSCKP
ParentalHGESTRN
..E.TRN
RetrocopyRDETTRN

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 .06 RPM 10 .14 RPM
bodymap2_adrenal 0 .00 RPM 22 .27 RPM
bodymap2_brain 0 .05 RPM 6 .96 RPM
bodymap2_breast 0 .00 RPM 14 .96 RPM
bodymap2_colon 0 .04 RPM 8 .22 RPM
bodymap2_heart 0 .15 RPM 16 .98 RPM
bodymap2_kidney 0 .00 RPM 18 .12 RPM
bodymap2_liver 0 .00 RPM 6 .06 RPM
bodymap2_lung 0 .04 RPM 6 .80 RPM
bodymap2_lymph_node 0 .00 RPM 18 .42 RPM
bodymap2_ovary 0 .02 RPM 17 .64 RPM
bodymap2_prostate 0 .00 RPM 12 .18 RPM
bodymap2_skeletal_muscle 0 .00 RPM 9 .31 RPM
bodymap2_testis 0 .00 RPM 9 .14 RPM
bodymap2_thyroid 0 .00 RPM 21 .15 RPM
bodymap2_white_blood_cells 0 .00 RPM 24 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_272 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_272 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_272 retrocopy 5' end.

Lab - click to see more details

retro_hsap_272 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_272 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_228
Gorilla gorilla retro_ggor_319
Pongo abelii retro_pabe_397
Macaca mulatta retro_mmul_567
Parental genes homology:
Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000045701 retrocopy
retro_cjac_1676,
Homo sapiens ENSG00000188917 1 retrocopy
retro_hsap_272 ,
Gorilla gorilla ENSGGOG000000237591 retrocopy
retro_ggor_319,
Macropus eugenii ENSMEUG000000065322 retrocopies
retro_meug_1325, retro_meug_74,
Macaca mulatta ENSMMUG000000103941 retrocopy
retro_mmul_567,
Monodelphis domestica ENSMODG000000256301 retrocopy
retro_mdom_77,
Nomascus leucogenys ENSNLEG000000075221 retrocopy
retro_nleu_1485,
Pongo abelii ENSPPYG000000205451 retrocopy
retro_pabe_397,
Pan troglodytes ENSPTRG000000234131 retrocopy
retro_ptro_228,

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 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 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 .03 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 .02 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 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 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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