RetrogeneDB ID:

retro_hsap_3846

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:51327128..51327858(-)
Located in intron of:ENSG00000106078
Retrocopy
information
Ensembl ID:ENSG00000231490
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7L1
Ensembl ID:ENSG00000146223
Aliases:RPL7L1, dJ475N16.4
Description:ribosomal protein L7-like 1 [Source:HGNC Symbol;Acc:21370]


Retrocopy-Parental alignment summary:






>retro_hsap_3846
GAGCAAGAGCAAAGAAAAATCCCTTTGGTTCCAGAAAATCTCCTGAAAAAGAGGAAGGCTTATCAAGTCCTCAAAGCCAC
CCAGGCAAAGCAGACACTTTTGGAGAAGAAGGAGCAGAGGAAAGGAAAAGGGCTCAAGTTAAACGACTGGAATCATTCCT
ATATGATTCCTGGTGGCAGAAACGTGACAAGATGCATCTCAGATGACTAGAAGTGAAACCTCATGCCTTGGAATTGCCAG
ATAACATTCCTTGGCCTTTATTGTACGCATTGAAAGGATTAATGACATGAGTTTACTGGTGCAGAGAACCATGGCAAGAC
TTCGCCTAAAGAAAATTTTTAGTGGTATCTTTGTAAAAGTCACCCCCCAGAACCTAAAAATGCTGCCCATAGTGGAAACT
TATGTGATCTGGGTATTTCCACATCTGAAGTCTGCCTGGGAACTCATTTTGAAATGTGGATGAGCCAAGGTCAAGAATAA
GACCATCCCTCAGACAGACAACACAGTGATGAGGAGCACCAGGGGAATTTTGGTGTCATTTGCTTGGAAGACCTCATTCA
TGAAATTGCCTTCCTGGAGAAGCATTTCCAGGAGATCTCATGGTTTTTGCGCCCTTTCCACTTCTCAGTGGCCCATCTTG
CTACCACAAATAGAGTGGGTTTCCTCAAGGAGATGGGCCCCACCTGGCTGTCGGGGTGAACACATCAATCAGCTCATCCA
CCAGCTGAAC

ORF - retro_hsap_3846 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.45 %
Parental protein coverage: 99.19 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalEQEQRKIPLVPENLLKKRKAYQALKATQAKQALLAKKEQKKGKGLRF-KRLESFLHDSWRQKRDKVRLRR
EQEQRKIPLVPENLLKKRKAYQ.LKATQAKQ.LL.KKEQ.KGKGL...KRLESFL.DSW.QKRDK..LR.
RetrocopyEQEQRKIPLVPENLLKKRKAYQVLKATQAKQTLLEKKEQRKGKGLKL<KRLESFLYDSWWQKRDKMHLR*
ParentalLEVKPHALELPDK-HSLAFVVRIERIDGVSLLVQRTIARLRLKKIFSGVFVKVTPQNLKMLRIVEPYVTW
LEVKPHALELPD..HSLAF.VRIERI...SLLVQRT.ARLRLKKIFSG.FVKVTPQNLKML.IVE.YV.W
RetrocopyLEVKPHALELPDN<HSLAFIVRIERINDMSLLVQRTMARLRLKKIFSGIFVKVTPQNLKMLPIVETYVIW
ParentalGFPNLKSVRELILKRGQAKVKNKTIPLTDNTVI-EEHLGKFGVICLEDLIHEIAFPGKHFQEISWFLCPF
.FP.LKS..ELILK.G.AKVKNKTIP.TDNTV..EEH.G.FGVICLEDLIHEIAF..KHFQEISWFL.PF
RetrocopyVFPHLKSAWELILKCG*AKVKNKTIPQTDNTVM<EEHQGNFGVICLEDLIHEIAFLEKHFQEISWFLRPF
ParentalHLSVARHATKNRVGFLKEMG-TPGYRGERINQLIRQLN
H.SVA..AT.NRVGFLKEMG..PG.RGE.INQLI.QLN
RetrocopyHFSVAHLATTNRVGFLKEMG>PPGCRGEHINQLIHQLN

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 71 .24 RPM
bodymap2_adrenal 0 .00 RPM 85 .66 RPM
bodymap2_brain 0 .00 RPM 66 .31 RPM
bodymap2_breast 0 .00 RPM 72 .96 RPM
bodymap2_colon 0 .00 RPM 69 .94 RPM
bodymap2_heart 0 .02 RPM 51 .54 RPM
bodymap2_kidney 0 .00 RPM 94 .84 RPM
bodymap2_liver 0 .00 RPM 76 .83 RPM
bodymap2_lung 0 .00 RPM 47 .63 RPM
bodymap2_lymph_node 0 .00 RPM 69 .64 RPM
bodymap2_ovary 0 .00 RPM 87 .92 RPM
bodymap2_prostate 0 .00 RPM 75 .95 RPM
bodymap2_skeletal_muscle 0 .00 RPM 43 .31 RPM
bodymap2_testis 0 .00 RPM 63 .35 RPM
bodymap2_thyroid 0 .00 RPM 105 .78 RPM
bodymap2_white_blood_cells 0 .00 RPM 81 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3846 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3846 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3846 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3846 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3846 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2622
Gorilla gorilla retro_ggor_2591
Pongo abelii retro_pabe_3053
Parental genes homology:
Parental genes homology involve 26 parental genes, and 165 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000127912 retrocopies
retro_amel_1260, retro_amel_243,
Bos taurus ENSBTAG000000184782 retrocopies
retro_btau_588, retro_btau_816,
Canis familiaris ENSCAFG000000017284 retrocopies
retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni ENSCHOG000000003064 retrocopies
retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus ENSCPOG000000211892 retrocopies
retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus ENSDNOG000000134851 retrocopy
retro_dnov_689,
Equus caballus ENSECAG000000031131 retrocopy
retro_ecab_998,
Erinaceus europaeus ENSEEUG000000104311 retrocopy
retro_eeur_90,
Echinops telfairi ENSETEG000000024193 retrocopies
retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus ENSFCAG000000097071 retrocopy
retro_fcat_143,
Homo sapiens ENSG00000146223 22 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 ENSG0000014760449 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,
Monodelphis domestica ENSMODG000000190281 retrocopy
retro_mdom_1708,
Mustela putorius furoENSMPUG000000132961 retrocopy
retro_mputfur_1577,
Mus musculus ENSMUSG000000638884 retrocopies
retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Nomascus leucogenys ENSNLEG0000000464921 retrocopies
retro_nleu_1375, retro_nleu_1597, retro_nleu_1646, retro_nleu_1661, retro_nleu_2007, retro_nleu_2011, retro_nleu_2017, retro_nleu_2138, retro_nleu_2201, retro_nleu_2282, retro_nleu_2562, retro_nleu_2599, retro_nleu_2694, retro_nleu_2863, retro_nleu_2938, retro_nleu_332, retro_nleu_502, retro_nleu_536, retro_nleu_597, retro_nleu_711, retro_nleu_727,
Otolemur garnettii ENSOGAG000000126713 retrocopies
retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pan troglodytes ENSPTRG0000001817523 retrocopies
retro_ptro_1074, retro_ptro_1088, retro_ptro_1127, retro_ptro_1162, retro_ptro_1671, retro_ptro_1849, retro_ptro_1927, retro_ptro_1987, retro_ptro_2069, retro_ptro_2076, retro_ptro_2198, retro_ptro_2257, retro_ptro_2293, retro_ptro_2416, retro_ptro_2466, retro_ptro_2622, retro_ptro_2686, retro_ptro_2916, retro_ptro_2933, retro_ptro_3212, retro_ptro_355, retro_ptro_878, retro_ptro_882,
Pteropus vampyrus ENSPVAG000000086963 retrocopies
retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus ENSRNOG000000162691 retrocopy
retro_rnor_2795,
Sorex araneus ENSSARG000000052862 retrocopies
retro_sara_100, retro_sara_211,
Sarcophilus harrisii ENSSHAG000000112191 retrocopy
retro_shar_216,
Sus scrofa ENSSSCG000000264723 retrocopies
retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus ENSSTOG000000098412 retrocopies
retro_itri_1233, retro_itri_417,
Tursiops truncatus ENSTTRG000000069716 retrocopies
retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos ENSVPAG000000088942 retrocopies
retro_vpac_386, retro_vpac_584,

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 ) 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 .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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