RetrogeneDB ID:

retro_hsap_3041

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:57186949..57187444(-)
Located in intron of:ENSG00000109265
Retrocopy
information
Ensembl ID:ENSG00000250324
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPL22
Ensembl ID:ENSG00000082515
Aliases:MRPL22, L22mt, MRP-L22, MRP-L25, RPML25
Description:mitochondrial ribosomal protein L22 [Source:HGNC Symbol;Acc:14480]


Retrocopy-Parental alignment summary:






>retro_hsap_3041
GGTCTCCTTCATCTCAGCATTTTACCCCAATCCCAGGTCCACACAAGTGCTTCTCTTGACACTTCTCAAAAATGGGAGAA
GAAGAATAAAACCGTTTATCCTCCACAACTGCCTGCAGAACCTCAGAGACCAGCAGAAATCTACCAATACCAAAGAAAAC
TAAAAGACAGCAAAGACAAGATGTTGTATTTGGCAAAATTGGTAGGAGAAATGTCCACTGACCAGGCTTAGCTCAACTGG
GATTCAGCGACAAAAAGGGACCCAAATCATTAAAGATGTTCTCTTAGAAGCACAAGACGTGGCAGTGAAAGACCACAATG
TGGAATTCAGATCTGGTTTATATATAAACTGAGTCCACCTCAGGGGGAGGCCAGTGCCTGACAGGCTTCTGCTACCAAAG
TAGAGGTTGCTTTGGGATCATGAAGGTTACTGCCATTATTTTATGAAGCTGGTGGAAGGGCCTCCCCACCTCCACGTGAG
GCACCCAAGATGGCG

ORF - retro_hsap_3041 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.09 %
Parental protein coverage: 71.55 %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalGKLALGVLPQSYIHTSASLDISRKWEKKNKIVYPPQLPGEPRRPAEIYHCRRQIKYSKDKMWYLAKLIRG
G.L.L..LPQS..HTSASLD.S.KWEKKNK.VYPPQLP.EP.RPAEIY...R..K.SKDKM.YLAKL...
RetrocopyGLLHLSILPQSQVHTSASLDTSQKWEKKNKTVYPPQLPAEPQRPAEIYQYQRKLKDSKDKMLYLAKLVGE
ParentalMSIDQA-LAQLEFNDKKGAK-IIKEVLLEAQDMAVRDHNVEFRSNLYI-AESTSGRGQCLKRIRYHGRGR
MS.DQA.LAQL.F.DKKG.K.IIK.VLLEAQD.AV.DHNVEFRS.LYI..ESTSG.GQCL....Y..RG.
RetrocopyMSTDQA<LAQLGFSDKKGPK<IIKDVLLEAQDVAVKDHNVEFRSGLYI>TESTSGGGQCLTGFCYQSRGC
ParentalFGIMEKV-YCHYFVKLVEGPP-PPP-EPPKTA
FGIM.KV.YCHYF.KLVEGPP.PPP.E.PK.A
RetrocopyFGIM-KV<YCHYFMKLVEGPP<PPPREAPKMA

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 16 .54 RPM
bodymap2_adrenal 0 .00 RPM 24 .65 RPM
bodymap2_brain 0 .00 RPM 14 .42 RPM
bodymap2_breast 0 .00 RPM 19 .44 RPM
bodymap2_colon 0 .00 RPM 19 .30 RPM
bodymap2_heart 0 .00 RPM 20 .58 RPM
bodymap2_kidney 0 .00 RPM 20 .62 RPM
bodymap2_liver 0 .00 RPM 20 .24 RPM
bodymap2_lung 0 .00 RPM 14 .43 RPM
bodymap2_lymph_node 0 .00 RPM 16 .32 RPM
bodymap2_ovary 0 .00 RPM 20 .30 RPM
bodymap2_prostate 0 .00 RPM 18 .31 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .80 RPM
bodymap2_testis 0 .00 RPM 31 .50 RPM
bodymap2_thyroid 0 .00 RPM 27 .40 RPM
bodymap2_white_blood_cells 0 .00 RPM 13 .17 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3041 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3041 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3041 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3041 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3041 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1997
Gorilla gorilla retro_ggor_2095
Pongo abelii retro_pabe_2436
Macaca mulatta retro_mmul_1889
Callithrix jacchus retro_cjac_2187
Parental genes homology:
Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000038751 retrocopy
retro_acar_88,
Callithrix jacchus ENSCJAG000000073252 retrocopies
retro_cjac_2187, retro_cjac_2558,
Homo sapiens ENSG00000082515 1 retrocopy
retro_hsap_3041 ,
Gorilla gorilla ENSGGOG000000102321 retrocopy
retro_ggor_2095,
Mus musculus ENSMUSG000000205141 retrocopy
retro_mmus_1294,
Nomascus leucogenys ENSNLEG000000166921 retrocopy
retro_nleu_1928,
Pongo abelii ENSPPYG000000159791 retrocopy
retro_pabe_2436,
Pan troglodytes ENSPTRG000000174531 retrocopy
retro_ptro_1997,

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 = 0.02 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 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 .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 .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 .02 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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