RetrogeneDB ID:

retro_hsap_2837

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:131962369..131963109(-)
Located in intron of:ENSG00000196353
Retrocopy
information
Ensembl ID:ENSG00000242899
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7
Ensembl ID:ENSG00000147604
Aliases:RPL7, L7, humL7-1
Description:ribosomal protein L7 [Source:HGNC Symbol;Acc:10363]


Retrocopy-Parental alignment summary:






>retro_hsap_2837
ATGGAGGGTGTTGAAGAGAAGAAGAAGGTTCCTGCTGTGCCAGAAACCCTTAAGAAAAAGTGAAGGAATTTCACAGAGCT
GAAGATCAAGCGCCTGAGAAATAAGTTTGCCCAAAAGATGCTTCTAAAGGCAAGGAGGAAGCTTATCTATGAAAAAGCAA
AGCACTATCACAAGGAATATATGCAGATGTACAGAACTGAAATTCAAATATCGAGGATGGCAAGAAAAGCTGGCAACTTC
TATGTATCTGCAGAACCCAAATTGGCGTTTGTCATCAGGATCGGAGGTTATCAATTGGGTGAGCCCAAAGGTCTGAAAGG
TGTTGCAACTTCTTTGCCTTCATCAAATCTTCAATAGAAACTTTGTGAAGCTCAGCAGGGCTTCAATAATGTGCTGAGGT
TTGTAGAACCATATATTGCATGGGCATACCCAAATCTGAAGTCAGTAAATAAACTAATCTACAAATGTGGTTATAGCAAA
ATGAATAAGAAGCTACTTGCTCCAACAGATAATACTTTGATTGCTCGATCTCTTGGTAAATATGGCCTCATCTGCATGGA
GGATCTGATTCATGAGATCTATACTGTTGGAAAATGCTTAAAGAAGCAAATAACTTCCTGTGGCCCTTCAAATTATCCTC
TCGACAAGTTAGAATGAAGAAAAAGACCACCAATTTTGTAGAAGGTGGAGATGCTGACAACAGGGAAGACCAGATCAACA
GGCTTATTAGAAGAATAAAC

ORF - retro_hsap_2837 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.87 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIR
MEGVEEKKK.VPAVPETLKKK.RNF.ELKIKRLR.KFAQKML.KARRKLIYEKAKHYHKEY.QMYRTEI.
RetrocopyMEGVEEKKK-VPAVPETLKKK*RNFTELKIKRLRNKFAQKMLLKARRKLIYEKAKHYHKEYMQMYRTEIQ
ParentalMARMARKAGNFYVPAEPKLAFVIRIRG-INGVSPKVRKVLQLLRLRQIFNGTFVKLNKASI-NMLRIVEP
..RMARKAGNFYV.AEPKLAFVIRI.G.IN.VSPKV.KVLQLL.L.QIFN..FVKL..ASI.N.LR.VEP
RetrocopyISRMARKAGNFYVSAEPKLAFVIRIGG>INWVSPKV*KVLQLLCLHQIFNRNFVKLSRASI<NVLRFVEP
ParentalYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVG-KRFKEANNF
YIAW.YPNLKSVN.LIYK.GY.K.NKK..A.TDN.LIARSLGKYG.ICMEDLIHEIYTVG.K..KEANNF
RetrocopyYIAWAYPNLKSVNKLIYKCGYSKMNKKLLAPTDNTLIARSLGKYGLICMEDLIHEIYTVG<KMLKEANNF
ParentalLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN
LWPFKLSS....MKKKTT.FVEGGDA.NREDQINRLIRR.N
RetrocopyLWPFKLSSRQVRMKKKTTNFVEGGDADNREDQINRLIRRIN

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 732 .70 RPM
bodymap2_adrenal 0 .00 RPM 756 .47 RPM
bodymap2_brain 0 .00 RPM 227 .86 RPM
bodymap2_breast 0 .00 RPM 671 .02 RPM
bodymap2_colon 0 .29 RPM 1010 .05 RPM
bodymap2_heart 0 .00 RPM 163 .75 RPM
bodymap2_kidney 0 .00 RPM 459 .62 RPM
bodymap2_liver 0 .00 RPM 197 .70 RPM
bodymap2_lung 0 .05 RPM 567 .88 RPM
bodymap2_lymph_node 0 .00 RPM 697 .27 RPM
bodymap2_ovary 0 .08 RPM 1313 .51 RPM
bodymap2_prostate 6 .89 RPM 945 .68 RPM
bodymap2_skeletal_muscle 0 .00 RPM 360 .36 RPM
bodymap2_testis 0 .34 RPM 532 .58 RPM
bodymap2_thyroid 0 .00 RPM 532 .91 RPM
bodymap2_white_blood_cells 0 .02 RPM 845 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2837 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2837 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_129158167 libraries118 libraries967 libraries426 libraries151 libraries

The graphical summary, for retro_hsap_2837 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2837 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2837 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 257 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000002013922 retrocopies
retro_btau_1088, retro_btau_1231, retro_btau_1367, retro_btau_1381, retro_btau_1422, retro_btau_1434, retro_btau_1468, retro_btau_1548, retro_btau_1559, retro_btau_1616, retro_btau_1627, retro_btau_1784, retro_btau_1814, retro_btau_304, retro_btau_426, retro_btau_622, retro_btau_668, retro_btau_730, retro_btau_750, retro_btau_758, retro_btau_863, retro_btau_879,
Callithrix jacchus ENSCJAG000000076861 retrocopy
retro_cjac_105,
Equus caballus ENSECAG000000091881 retrocopy
retro_ecab_35,
Homo sapiens ENSG0000014622322 retrocopies
retro_hsap_1285, retro_hsap_1291, retro_hsap_1602, retro_hsap_1623, retro_hsap_1661, retro_hsap_1836, retro_hsap_2201, retro_hsap_2389, retro_hsap_2735, retro_hsap_2845, retro_hsap_3053, retro_hsap_3068, retro_hsap_3077, retro_hsap_3187, retro_hsap_3250, retro_hsap_3373, retro_hsap_3556, retro_hsap_3641, retro_hsap_3846, retro_hsap_3957, retro_hsap_4770, retro_hsap_4827,
Homo sapiens ENSG00000147604 49 retrocopies
retro_hsap_1001, retro_hsap_1023, retro_hsap_1033, retro_hsap_1034, retro_hsap_1128, retro_hsap_113, retro_hsap_1232, retro_hsap_1281, retro_hsap_1614, retro_hsap_1626, retro_hsap_1844, retro_hsap_1862, retro_hsap_1957, retro_hsap_2008, retro_hsap_203, retro_hsap_2093, retro_hsap_2101, retro_hsap_2588, retro_hsap_2837 , retro_hsap_3197, retro_hsap_3204, retro_hsap_3244, retro_hsap_3254, retro_hsap_3356, retro_hsap_3399, retro_hsap_344, retro_hsap_3453, retro_hsap_3493, retro_hsap_3560, retro_hsap_3573, retro_hsap_3625, retro_hsap_3717, retro_hsap_3775, retro_hsap_3883, retro_hsap_3918, retro_hsap_4137, retro_hsap_415, retro_hsap_426, retro_hsap_4306, retro_hsap_4662, retro_hsap_4704, retro_hsap_4718, retro_hsap_4761, retro_hsap_558, retro_hsap_616, retro_hsap_708, retro_hsap_729, retro_hsap_973, retro_hsap_976,
Latimeria chalumnae ENSLACG000000035711 retrocopy
retro_lcha_63,
Macropus eugenii ENSMEUG000000163199 retrocopies
retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Microcebus murinus ENSMICG000000028808 retrocopies
retro_mmur_1170, retro_mmur_1379, retro_mmur_139, retro_mmur_158, retro_mmur_52, retro_mmur_596, retro_mmur_646, retro_mmur_903,
Macaca mulatta ENSMMUG000000051411 retrocopy
retro_mmul_129,
Monodelphis domestica ENSMODG000000071364 retrocopies
retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Otolemur garnettii ENSOGAG000000039032 retrocopies
retro_ogar_15, retro_ogar_225,
Pongo abelii ENSPPYG0000001867150 retrocopies
retro_pabe_1025, retro_pabe_1061, retro_pabe_1087, retro_pabe_1326, retro_pabe_1454, retro_pabe_1520, retro_pabe_1642, retro_pabe_1677, retro_pabe_1908, retro_pabe_1998, retro_pabe_2004, retro_pabe_2118, retro_pabe_2197, retro_pabe_2348, retro_pabe_2656, retro_pabe_2690, retro_pabe_2762, retro_pabe_2796, retro_pabe_2807, retro_pabe_2808, retro_pabe_2856, retro_pabe_2886, retro_pabe_2936, retro_pabe_2946, retro_pabe_307, retro_pabe_3085, retro_pabe_3117, retro_pabe_3139, retro_pabe_3191, retro_pabe_3414, retro_pabe_3468, retro_pabe_3506, retro_pabe_352, retro_pabe_3622, retro_pabe_3651, retro_pabe_3662, retro_pabe_3669, retro_pabe_3675, retro_pabe_436, retro_pabe_497, retro_pabe_514, retro_pabe_551, retro_pabe_628, retro_pabe_655, retro_pabe_826, retro_pabe_844, retro_pabe_859, retro_pabe_865, retro_pabe_867, retro_pabe_933,
Rattus norvegicus ENSRNOG0000000699227 retrocopies
retro_rnor_1018, retro_rnor_1174, retro_rnor_1222, retro_rnor_1233, retro_rnor_1307, retro_rnor_1388, retro_rnor_1466, retro_rnor_1580, retro_rnor_1745, retro_rnor_1916, retro_rnor_1944, retro_rnor_2025, retro_rnor_2028, retro_rnor_2100, retro_rnor_2247, retro_rnor_2304, retro_rnor_2347, retro_rnor_2531, retro_rnor_2715, retro_rnor_2765, retro_rnor_2814, retro_rnor_2824, retro_rnor_530, retro_rnor_666, retro_rnor_911, retro_rnor_929, retro_rnor_977,
Ictidomys tridecemlineatus ENSSTOG0000000458618 retrocopies
retro_itri_1025, retro_itri_1080, retro_itri_1358, retro_itri_1375, retro_itri_1412, retro_itri_1430, retro_itri_1464, retro_itri_1593, retro_itri_1776, retro_itri_271, retro_itri_346, retro_itri_349, retro_itri_351, retro_itri_390, retro_itri_534, retro_itri_542, retro_itri_827, retro_itri_917,
Tupaia belangeri ENSTBEG000000023011 retrocopy
retro_tbel_2042,
Tarsius syrichta ENSTSYG0000000610025 retrocopies
retro_tsyr_1149, retro_tsyr_1200, retro_tsyr_1293, retro_tsyr_1297, retro_tsyr_1403, retro_tsyr_1598, retro_tsyr_1633, retro_tsyr_1850, retro_tsyr_1891, retro_tsyr_191, retro_tsyr_2109, retro_tsyr_2130, retro_tsyr_344, retro_tsyr_421, retro_tsyr_433, retro_tsyr_521, retro_tsyr_589, retro_tsyr_601, retro_tsyr_651, retro_tsyr_724, retro_tsyr_779, retro_tsyr_877, retro_tsyr_930, retro_tsyr_953, retro_tsyr_992,
Tursiops truncatus ENSTTRG0000000907416 retrocopies
retro_ttru_1241, retro_ttru_1546, retro_ttru_1690, retro_ttru_174, retro_ttru_1776, retro_ttru_1918, retro_ttru_210, retro_ttru_290, retro_ttru_367, retro_ttru_402, retro_ttru_534, retro_ttru_604, retro_ttru_726, retro_ttru_852, retro_ttru_933, retro_ttru_952,

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 = 0.03 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 .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 .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 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 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 .02 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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