RetrogeneDB ID:

retro_hsap_2939

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:66439176..66440043(+)
Located in intron of:ENSG00000145242
Retrocopy
information
Ensembl ID:ENSG00000243199
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL6
Ensembl ID:ENSG00000089009
Aliases:RPL6, L6, SHUJUN-2, TAXREB107, TXREB1
Description:ribosomal protein L6 [Source:HGNC Symbol;Acc:10362]


Retrocopy-Parental alignment summary:






>retro_hsap_2939
ATGGCGGGTGAAAAAGTTTAGAAGCCAGATACTAAAGAGAAGAAACCCGAAGCCAAGAAGACTGATGCTGGTGGCAAGGT
GAAAAAGGGTAACCTCAAAGCTAAAAAGCCCAAGAAGGGGAAGCCCCGTTGCAGCCGCAACCCTGTCCTTGTCAGAGGAA
TTGGCAGGTATTCCCGATCTGCCATGTATTCCAGAAAGGCCATGTACAAGAGGAAGTACTCAGCCGCTAAATCCAAGGTT
GAAAAGAAAAAGAAGGAGAAGGTTCTTGCAACTGTTACAAAACCAGTTGGTGGTGACAAGAACGGCGGTACCCGGGTGGT
TAAACTTCGCAAAATGCCTAGATATTATCCTACTGAAGATGTGCCTCGAAAGCTGTTGAGCCACGGCAAAAAAAAACCCT
TCAGTCAGCACGTGAGAAAACTGCGAGCCAGCATTACCCCCGGGACCATTCTGATCATCCTCACTGGACGCCACAGGGGC
AAGAGGGTGGTTTTCCTGAAGCAGCTGGCTAGTGGCTTATTACTTGTGACTGGACCTCTGGTCCTCAATCGAGTTCCTCT
ATGAAGAACACACCAGAAATTTGTCATTGCCACCTCAACCAAAATCGATATCAGCAATGTAAAAATCCCAAAACATCTTA
CTGATGCTTACTTCAAGAAGAAGCAGCTGCGGAAGCCCAGACACCAGGAAGGTGAGATCTTCGACACAGAAAAAGGGAAA
TATGAGATTACGGAGCAGCGCAAGATTGATCAGAAAGCTGTGGACTCACAAATTTTATCAAAAATCAAAGCTATTCCTCA
GCTCCAGGGCTAGTTGCGATCTGTGTTTGCCCTGACGAATGGAATTTATCCTCACAAATTGGTGTTC

ORF - retro_hsap_2939 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.19 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 3
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAGEKVEKPDTKEKKPEAKKVDAGGKVKKGNLKAKKPKKGKPHCSRNPVLVRGIGRYSRSAMYSRKAMYK
MAGEKV.KPDTKEKKPEAKK.DAGGKVKKGNLKAKKPKKGKP.CSRNPVLVRGIGRYSRSAMYSRKAMYK
RetrocopyMAGEKV*KPDTKEKKPEAKKTDAGGKVKKGNLKAKKPKKGKPRCSRNPVLVRGIGRYSRSAMYSRKAMYK
ParentalRKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKK-PFSQHVRK
RKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHG...PFSQHVRK
RetrocopyRKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGXXXPFSQHVRK
ParentalLRASITPGTILIILTGRHRGKRVVFLKQLASGLLLVTGPLVLNRVPLRRTHQKFVIATSTKIDISNVKIP
LRASITPGTILIILTGRHRGKRVVFLKQLASGLLLVTGPLVLNRVPL.RTHQKFVIATSTKIDISNVKIP
RetrocopyLRASITPGTILIILTGRHRGKRVVFLKQLASGLLLVTGPLVLNRVPL*RTHQKFVIATSTKIDISNVKIP
ParentalKHLTDAYFKKKKLRKPRHQEGEIFDTEKEKYEITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSVFALTN
KHLTDAYFKKK.LRKPRHQEGEIFDTEK.KYEITEQRKIDQKAVDSQIL.KIKAIPQLQG.LRSVFALTN
RetrocopyKHLTDAYFKKKQLRKPRHQEGEIFDTEKGKYEITEQRKIDQKAVDSQILSKIKAIPQLQG*LRSVFALTN
ParentalGIYPHKLVF
GIYPHKLVF
RetrocopyGIYPHKLVF

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 1 .95 RPM 476 .10 RPM
bodymap2_adrenal 3 .44 RPM 699 .56 RPM
bodymap2_brain 0 .09 RPM 206 .53 RPM
bodymap2_breast 1 .48 RPM 440 .47 RPM
bodymap2_colon 1 .33 RPM 761 .83 RPM
bodymap2_heart 0 .35 RPM 153 .63 RPM
bodymap2_kidney 1 .26 RPM 364 .93 RPM
bodymap2_liver 0 .19 RPM 285 .99 RPM
bodymap2_lung 1 .53 RPM 494 .64 RPM
bodymap2_lymph_node 1 .41 RPM 800 .90 RPM
bodymap2_ovary 2 .62 RPM 879 .55 RPM
bodymap2_prostate 1 .80 RPM 824 .70 RPM
bodymap2_skeletal_muscle 0 .53 RPM 237 .75 RPM
bodymap2_testis 1 .00 RPM 394 .46 RPM
bodymap2_thyroid 1 .21 RPM 557 .99 RPM
bodymap2_white_blood_cells 2 .09 RPM 915 .35 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_2939 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2939 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2939 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2939 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2939 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 157 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000030601 retrocopy
retro_acar_171,
Bos taurus ENSBTAG000000317236 retrocopies
retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris ENSCAFG000000088731 retrocopy
retro_cfam_36,
Callithrix jacchus ENSCJAG000000124507 retrocopies
retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus ENSCPOG000000135268 retrocopies
retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Dipodomys ordii ENSDORG000000057931 retrocopy
retro_dord_166,
Equus caballus ENSECAG000000175141 retrocopy
retro_ecab_811,
Erinaceus europaeus ENSEEUG000000002813 retrocopies
retro_eeur_503, retro_eeur_553, retro_eeur_595,
Felis catus ENSFCAG0000000685812 retrocopies
retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Homo sapiens ENSG00000089009 26 retrocopies
retro_hsap_1035, retro_hsap_146, retro_hsap_1905, retro_hsap_2074, retro_hsap_2164, retro_hsap_2206, retro_hsap_227, retro_hsap_2566, retro_hsap_2720, retro_hsap_2725, retro_hsap_2939 , retro_hsap_2955, retro_hsap_3009, retro_hsap_3014, retro_hsap_3070, retro_hsap_333, retro_hsap_3431, retro_hsap_3559, retro_hsap_3795, retro_hsap_3818, retro_hsap_3856, retro_hsap_4039, retro_hsap_440, retro_hsap_4729, retro_hsap_4788, retro_hsap_648,
Gorilla gorilla ENSGGOG0000000337216 retrocopies
retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Macaca mulatta ENSMMUG000000074331 retrocopy
retro_mmul_171,
Monodelphis domestica ENSMODG000000030964 retrocopies
retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furoENSMPUG000000025269 retrocopies
retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus ENSMUSG0000002961413 retrocopies
retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys ENSNLEG000000270932 retrocopies
retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus ENSOCUG000000038025 retrocopies
retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Pongo abelii ENSPPYG0000002585513 retrocopies
retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus ENSRNOG000000259361 retrocopy
retro_rnor_129,
Sarcophilus harrisii ENSSHAG000000070962 retrocopies
retro_shar_506, retro_shar_536,
Ictidomys tridecemlineatus ENSSTOG000000094093 retrocopies
retro_itri_1024, retro_itri_1125, retro_itri_684,
Tarsius syrichta ENSTSYG0000000949222 retrocopies
retro_tsyr_1046, retro_tsyr_1254, retro_tsyr_1600, retro_tsyr_1615, retro_tsyr_2052, retro_tsyr_2080, retro_tsyr_2123, retro_tsyr_2126, retro_tsyr_291, retro_tsyr_362, retro_tsyr_364, retro_tsyr_438, retro_tsyr_477, retro_tsyr_490, retro_tsyr_566, retro_tsyr_586, retro_tsyr_626, retro_tsyr_637, retro_tsyr_774, retro_tsyr_833, retro_tsyr_894, retro_tsyr_923,

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 = 6.94 RPM Legend:


Library Retrogene expression
CEU_NA11831 4 .02 RPM
CEU_NA11843 3 .16 RPM
CEU_NA11930 6 .94 RPM
CEU_NA12004 1 .48 RPM
CEU_NA12400 5 .23 RPM
CEU_NA12751 4 .64 RPM
CEU_NA12760 6 .56 RPM
CEU_NA12827 5 .94 RPM
CEU_NA12872 3 .51 RPM
CEU_NA12873 4 .85 RPM
FIN_HG00183 6 .18 RPM
FIN_HG00277 3 .55 RPM
FIN_HG00315 5 .38 RPM
FIN_HG00321 3 .90 RPM
FIN_HG00328 2 .60 RPM
FIN_HG00338 4 .22 RPM
FIN_HG00349 4 .13 RPM
FIN_HG00375 2 .18 RPM
FIN_HG00377 3 .45 RPM
FIN_HG00378 4 .78 RPM
GBR_HG00099 3 .23 RPM
GBR_HG00111 3 .83 RPM
GBR_HG00114 2 .47 RPM
GBR_HG00119 4 .12 RPM
GBR_HG00131 4 .31 RPM
GBR_HG00133 4 .51 RPM
GBR_HG00134 1 .38 RPM
GBR_HG00137 1 .87 RPM
GBR_HG00142 1 .44 RPM
GBR_HG00143 4 .91 RPM
TSI_NA20512 3 .11 RPM
TSI_NA20513 2 .30 RPM
TSI_NA20518 2 .66 RPM
TSI_NA20532 5 .27 RPM
TSI_NA20538 3 .78 RPM
TSI_NA20756 6 .26 RPM
TSI_NA20765 3 .58 RPM
TSI_NA20771 6 .50 RPM
TSI_NA20786 2 .35 RPM
TSI_NA20798 2 .68 RPM
YRI_NA18870 2 .67 RPM
YRI_NA18907 1 .94 RPM
YRI_NA18916 6 .21 RPM
YRI_NA19093 3 .64 RPM
YRI_NA19099 3 .59 RPM
YRI_NA19114 4 .33 RPM
YRI_NA19118 4 .18 RPM
YRI_NA19213 2 .92 RPM
YRI_NA19214 0 .89 RPM
YRI_NA19223 2 .90 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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