RetrogeneDB ID:

retro_hsap_2600

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:50151941..50152628(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000214727
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL5
Ensembl ID:ENSG00000122406
Aliases:RPL5, DBA6, L5
Description:ribosomal protein L5 [Source:HGNC Symbol;Acc:10360]


Retrocopy-Parental alignment summary:






>retro_hsap_2600
ATGGGGTTTGTTAAAATTAAGAATAAGGCCTGCTTTAAGAGATACCAAGTGAAATTTAGACGATGAGGCGAGGGTAAAAC
TGATCACTATGCTCAGAAACATTTGGTGATACAGGATAAAAATAAACACCACATATCCAAATACAGGATGATAGTTTGTG
TAACAAACAGAGATATCATTTGTTAGATTGCTTATGCCCGTATAGAGGGGGATATGATAGTCTGTGTAGCATATGCACAC
GAACTGCCAAAATATAGTGTGAAGGTTGGCCTGACAAATGACACTGCAGTGTATTGTCCTGGCCTGCTGCTGGCCCGCAG
GCTTCTCAATAGGTTTGGCCTGGACAAGATCTAAGAAGGCCAAGTGGAGGTGACTGGCGATGAATACAGTGTGGAGAGCA
TAGATGGTCAGCTGGGTGCCTTTGTCTACTCTTTGGATGCAGAGCTTGCCAGAACTGCCGCTGGCAATAAAGTTTTTGGT
GCCCTAAAGGGAGCTGTGGATGGAGGCTGGTCTGTCCCTCACGGTACCAAACAATTCCCTGGTCATGATTCTGAAAGCAA
AGAATTTAATGCAGAAGTACACTGGAAGCACATCATAGGCCAGAATGTTGCAGATTACATGCGTTACTTAATGGAGGAAG
ATGAAGATGCTTACAAGAAACTCTCTCAATACATAAAGAACAGGGTA

ORF - retro_hsap_2600 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.68 %
Parental protein coverage: 77.78 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIE
MGFVK..KNKA.FKRYQVKFRR..EGKTD.YA.K.LVIQDKNK....KYRMIV.VTNRDIIC.IAYARIE
RetrocopyMGFVKI-KNKACFKRYQVKFRR*GEGKTDHYAQKHLVIQDKNKHHISKYRMIVCVTNRDIIC*IAYARIE
ParentalGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPG
GDMIVC.AYAHELPKY.VKVGLTN..A.YC.GLLLARRLLNRFG.DKI.EGQVEVTGDEY.VESIDGQ.G
RetrocopyGDMIVCVAYAHELPKYSVKVGLTNDTAVYCPGLLLARRLLNRFGLDKI*EGQVEVTGDEYSVESIDGQLG
ParentalAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRY
AF...LDA.LART..GNKVFGALKGAVDGG.S.PH.TK.FPG.DSESKEFNAEVH.KHI.GQNVADYMRY
RetrocopyAFVYSLDAELARTAAGNKVFGALKGAVDGGWSVPHGTKQFPGHDSESKEFNAEVHWKHIIGQNVADYMRY
ParentalLMEEDEDAYKKQFSQYIKNSV
LMEEDEDAYKK..SQYIKN.V
RetrocopyLMEEDEDAYKK-LSQYIKNRV

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 831 .47 RPM
bodymap2_adrenal 0 .00 RPM 1088 .69 RPM
bodymap2_brain 0 .00 RPM 287 .02 RPM
bodymap2_breast 0 .00 RPM 690 .73 RPM
bodymap2_colon 0 .00 RPM 1255 .57 RPM
bodymap2_heart 0 .00 RPM 286 .90 RPM
bodymap2_kidney 0 .00 RPM 467 .21 RPM
bodymap2_liver 0 .00 RPM 264 .66 RPM
bodymap2_lung 0 .00 RPM 964 .12 RPM
bodymap2_lymph_node 0 .00 RPM 1025 .32 RPM
bodymap2_ovary 0 .00 RPM 2109 .24 RPM
bodymap2_prostate 0 .00 RPM 1546 .91 RPM
bodymap2_skeletal_muscle 0 .02 RPM 345 .73 RPM
bodymap2_testis 0 .00 RPM 860 .64 RPM
bodymap2_thyroid 0 .08 RPM 950 .21 RPM
bodymap2_white_blood_cells 0 .00 RPM 1265 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2600 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2600 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2600 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2600 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2600 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1524
Parental genes homology:
Parental genes homology involve 14 parental genes, and 141 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG000000028521 retrocopy
retro_eeur_620,
Echinops telfairi ENSETEG000000098898 retrocopies
retro_etel_1044, retro_etel_1089, retro_etel_1103, retro_etel_1264, retro_etel_2028, retro_etel_64, retro_etel_785, retro_etel_814,
Homo sapiens ENSG00000122406 30 retrocopies
retro_hsap_1266, retro_hsap_138, retro_hsap_1469, retro_hsap_1539, retro_hsap_1588, retro_hsap_1767, retro_hsap_183, retro_hsap_1989, retro_hsap_2143, retro_hsap_2385, retro_hsap_2594, retro_hsap_2600 , retro_hsap_2777, retro_hsap_2962, retro_hsap_3105, retro_hsap_3178, retro_hsap_3181, retro_hsap_3209, retro_hsap_3430, retro_hsap_3520, retro_hsap_3941, retro_hsap_4048, retro_hsap_4104, retro_hsap_486, retro_hsap_590, retro_hsap_632, retro_hsap_646, retro_hsap_742, retro_hsap_780, retro_hsap_827,
Gorilla gorilla ENSGGOG0000000269924 retrocopies
retro_ggor_1129, retro_ggor_1172, retro_ggor_1206, retro_ggor_1342, retro_ggor_1343, retro_ggor_1656, retro_ggor_1934, retro_ggor_2052, retro_ggor_2130, retro_ggor_2178, retro_ggor_2243, retro_ggor_2318, retro_ggor_233, retro_ggor_2380, retro_ggor_264, retro_ggor_2649, retro_ggor_2715, retro_ggor_2755, retro_ggor_457, retro_ggor_521, retro_ggor_553, retro_ggor_622, retro_ggor_647, retro_ggor_996,
Macropus eugenii ENSMEUG000000063613 retrocopies
retro_meug_1168, retro_meug_1537, retro_meug_2146,
Myotis lucifugus ENSMLUG000000089561 retrocopy
retro_mluc_925,
Monodelphis domestica ENSMODG000000116351 retrocopy
retro_mdom_748,
Nomascus leucogenys ENSNLEG000000105002 retrocopies
retro_nleu_2102, retro_nleu_39,
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
retro_oana_97,
Otolemur garnettii ENSOGAG000000132466 retrocopies
retro_ogar_1164, retro_ogar_134, retro_ogar_1627, retro_ogar_2374, retro_ogar_2633, retro_ogar_707,
Petromyzon marinus ENSPMAG000000020401 retrocopy
retro_pmar_23,
Pongo abelii ENSPPYG0000000115232 retrocopies
retro_pabe_1053, retro_pabe_1219, retro_pabe_1274, retro_pabe_1307, retro_pabe_1331, retro_pabe_1501, retro_pabe_1918, retro_pabe_1931, retro_pabe_2019, retro_pabe_2123, retro_pabe_2238, retro_pabe_2457, retro_pabe_246, retro_pabe_247, retro_pabe_2640, retro_pabe_2641, retro_pabe_2658, retro_pabe_2813, retro_pabe_2841, retro_pabe_2909, retro_pabe_3247, retro_pabe_3320, retro_pabe_3360, retro_pabe_3534, retro_pabe_446, retro_pabe_447, retro_pabe_480, retro_pabe_51, retro_pabe_562, retro_pabe_572, retro_pabe_637, retro_pabe_740,
Pan troglodytes ENSPTRG0000000096330 retrocopies
retro_ptro_1038, retro_ptro_1068, retro_ptro_1184, retro_ptro_1326, retro_ptro_139, retro_ptro_1519, retro_ptro_1524, retro_ptro_1568, retro_ptro_169, retro_ptro_1744, retro_ptro_1878, retro_ptro_2005, retro_ptro_2241, retro_ptro_2262, retro_ptro_2264, retro_ptro_2329, retro_ptro_2391, retro_ptro_2674, retro_ptro_2742, retro_ptro_2785, retro_ptro_2941, retro_ptro_3027, retro_ptro_366, retro_ptro_433, retro_ptro_460, retro_ptro_470, retro_ptro_528, retro_ptro_577, retro_ptro_866, retro_ptro_997,
Sarcophilus harrisii ENSSHAG000000064171 retrocopy
retro_shar_202,

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 .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 .05 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 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 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 .02 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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