RetrogeneDB ID:

retro_hsap_323

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:235901305..235902286(+)
Located in intron of:ENSG00000143669
Retrocopy
information
Ensembl ID:ENSG00000235674
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHA
Ensembl ID:ENSG00000134333
Aliases:LDHA, GSD11, HEL-S-133P, LDH1, LDHM
Description:lactate dehydrogenase A [Source:HGNC Symbol;Acc:6535]


Retrocopy-Parental alignment summary:






>retro_hsap_323
ACGCTCAAGGATCAGCTTATTCACAGTCTTCTAAAGGAAGAACAGATCCTCCAGAATAAGATTACAGTTGTTGGGGTTGG
TGCTCTTGGCATGGCCTGTGCCATCGGTATCTTAATGAAGGACTTGGCAGGCGAACTTGCTCTTGTTGATGTCATGGAAG
ACAAATTGAAGGGCGAGATGATGGATCTCCACCATGGCAGCCTTTTCCTTAGAACACCAAAGATTGTCTCTGGCAAAGAC
TATACTGTAACTGTAAACTCCAAGCTGGTCACTATCACGGCTGAGGCACATCGCAAGAGGGAGAAAGCCATCTTAATTTG
GTCCAGTGTAATGTGAACATCTTTAAATTCATCATTCCTAATGTTGTAAAATACAGCCCGAACTGCAAGTTGCTTATTGT
TTCAAATCCAGTGGATATCTTTGACCTATAGTGGCTTGGAAGATAATGGCTTTCCCAAAAACCATGTTATTGGAAGTGGT
TGCAATCTGGACTCAGCCCAATTCCGTTACCCAATGGGGGAAAGGCTGGGAGTTCACACATTAAGCTGTCATGGGTGAGT
CCTTGGGGAACATGGAGATTCTAGTGTGCCTGTATGGAGTAAAGCAAATGTTACTGGTGTCTCCCTCAAGACTCTGCACC
CAGATTTAGGGACTGACATAGATAAGGAACAGTGGAAAGAGGTTCACAAGCAGGTGGTTGAGAGTGCTTACGAGGTGATC
AAACTCAAAGGCTACACATCCTGGGCCATTGGACTCTCTGTGGCAGATTTGGCAGAAAGTATAATGAAGAATCTTAGGCG
GGTGCACCCAATTTCCACCATGATTGGTGGAATAAAGGATGATGTCTTCCTTAGCATTCCTTGCATCTTGGGAGAGAATG
GAATCTCAGACCGTGTGAAGGTGACTCTGACTCCTGAGGAAGGGGCCCATTTGAAGAACAGTGCAGATCCACTTTGGGGG
ATACAAAAAGAGCTGCAATTT

ORF - retro_hsap_323 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.83 %
Parental protein coverage: 99.4 %
Number of stop codons detected: 1
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalTLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFL
TLKDQLI..LLKEEQ..QNKITVVGVGA.GMACAI.ILMKDLA.ELALVDV.EDKLKGEMMDL.HGSLFL
RetrocopyTLKDQLIHSLLKEEQILQNKITVVGVGALGMACAIGILMKDLAGELALVDVMEDKLKGEMMDLHHGSLFL
ParentalRTPKIVSGKDYNVTANSKLVIITAGARQ-QEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVD
RTPKIVSGKDY.VT.NSKLV.ITA.A...QEGES.LNLVQ.NVNIFKFIIPNVVKYSPNCKLLIVSNPVD
RetrocopyRTPKIVSGKDYTVTVNSKLVTITAEAHR<QEGESHLNLVQCNVNIFKFIIPNVVKYSPNCKLLIVSNPVD
ParentalI-LTY-VAWKI-SGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAG
I.LTY.VAWKI..GFPKN.VIGSGCNLDSA.FRY.MGERLGVH.LSCHG.VLGEHGDSSVPVWS..NV.G
RetrocopyI>LTY>VAWKI<NGFPKNHVIGSGCNLDSAQFRYPMGERLGVHTLSCHG*VLGEHGDSSVPVWSKANVTG
ParentalVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIK
VSLKTLHPDLGTD.DKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHP.STMI.
RetrocopyVSLKTLHPDLGTDIDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIG
ParentalGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF
G...IKDDVFLS.PCILG.NGISD.VKVTLT.EE.A.LK.SAD.LWGIQKELQF
RetrocopyG---IKDDVFLSIPCILGENGISDRVKVTLTPEEGAHLKNSADPLWGIQKELQF

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 .56 RPM 677 .74 RPM
bodymap2_adrenal 1 .78 RPM 652 .87 RPM
bodymap2_brain 0 .70 RPM 293 .75 RPM
bodymap2_breast 0 .58 RPM 877 .38 RPM
bodymap2_colon 0 .12 RPM 653 .53 RPM
bodymap2_heart 0 .20 RPM 275 .86 RPM
bodymap2_kidney 0 .17 RPM 797 .94 RPM
bodymap2_liver 0 .27 RPM 1282 .88 RPM
bodymap2_lung 1 .35 RPM 554 .06 RPM
bodymap2_lymph_node 1 .46 RPM 571 .34 RPM
bodymap2_ovary 0 .19 RPM 423 .80 RPM
bodymap2_prostate 0 .31 RPM 470 .43 RPM
bodymap2_skeletal_muscle 0 .02 RPM 208 .47 RPM
bodymap2_testis 0 .43 RPM 412 .13 RPM
bodymap2_thyroid 0 .47 RPM 621 .92 RPM
bodymap2_white_blood_cells 4 .88 RPM 246 .29 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_323 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_323 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_323 retrocopy 5' end.

Lab - click to see more details

retro_hsap_323 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_323 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_259
Pongo abelii retro_pabe_364
Parental genes homology:
Parental genes homology involve 28 parental genes, and 224 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178542 retrocopies
retro_amel_389, retro_amel_462,
Bos taurus ENSBTAG000000086832 retrocopies
retro_btau_1715, retro_btau_1822,
Choloepus hoffmanni ENSCHOG0000000997714 retrocopies
retro_chof_1038, retro_chof_144, retro_chof_1489, retro_chof_1524, retro_chof_1547, retro_chof_172, retro_chof_1874, retro_chof_2121, retro_chof_217, retro_chof_2365, retro_chof_2588, retro_chof_2611, retro_chof_552, retro_chof_990,
Callithrix jacchus ENSCJAG000000070941 retrocopy
retro_cjac_2290,
Cavia porcellus ENSCPOG000000119262 retrocopies
retro_cpor_1055, retro_cpor_427,
Dasypus novemcinctus ENSDNOG0000001891511 retrocopies
retro_dnov_1063, retro_dnov_1366, retro_dnov_1429, retro_dnov_1707, retro_dnov_1848, retro_dnov_2417, retro_dnov_362, retro_dnov_669, retro_dnov_797, retro_dnov_821, retro_dnov_887,
Equus caballus ENSECAG000000206695 retrocopies
retro_ecab_1004, retro_ecab_765, retro_ecab_837, retro_ecab_924, retro_ecab_933,
Echinops telfairi ENSETEG0000000750815 retrocopies
retro_etel_1091, retro_etel_1192, retro_etel_1243, retro_etel_1309, retro_etel_1439, retro_etel_1609, retro_etel_1870, retro_etel_1916, retro_etel_1969, retro_etel_1996, retro_etel_2209, retro_etel_361, retro_etel_392, retro_etel_828, retro_etel_884,
Homo sapiens ENSG000001117161 retrocopy
retro_hsap_4863,
Homo sapiens ENSG00000134333 5 retrocopies
retro_hsap_2097, retro_hsap_2285, retro_hsap_3021, retro_hsap_323 , retro_hsap_4231,
Homo sapiens ENSG000001668002 retrocopies
retro_hsap_42, retro_hsap_905,
Gorilla gorilla ENSGGOG000000103503 retrocopies
retro_ggor_1698, retro_ggor_349, retro_ggor_619,
Loxodonta africana ENSLAFG000000113071 retrocopy
retro_lafr_11,
Macropus eugenii ENSMEUG0000000146291 retrocopies
retro_meug_101, retro_meug_1029, retro_meug_103, retro_meug_1082, retro_meug_1088, retro_meug_1105, retro_meug_1140, retro_meug_1162, retro_meug_1189, retro_meug_1190, retro_meug_1260, retro_meug_1288, retro_meug_1295, retro_meug_1301, retro_meug_1323, retro_meug_1329, retro_meug_1332, retro_meug_1356, retro_meug_1368, retro_meug_1376, retro_meug_1400, retro_meug_1402, retro_meug_1404, retro_meug_1417, retro_meug_1419, retro_meug_1420, retro_meug_1422, retro_meug_1484, retro_meug_1535, retro_meug_155, retro_meug_1556, retro_meug_1620, retro_meug_1632, retro_meug_1652, retro_meug_1674, retro_meug_1685, retro_meug_1720, retro_meug_1721, retro_meug_1747, retro_meug_1749, retro_meug_1765, retro_meug_1779, retro_meug_1781, retro_meug_181, retro_meug_1824, retro_meug_1875, retro_meug_1898, retro_meug_1906, retro_meug_1915, retro_meug_1927, retro_meug_1945, retro_meug_1977, retro_meug_200, retro_meug_2000, retro_meug_2022, retro_meug_2067, retro_meug_2107, retro_meug_2126, retro_meug_2137, retro_meug_2139, retro_meug_2168, retro_meug_226, retro_meug_244, retro_meug_291, retro_meug_336, retro_meug_351, retro_meug_436, retro_meug_448, retro_meug_477, retro_meug_532, retro_meug_572, retro_meug_590, retro_meug_591, retro_meug_626, retro_meug_634, retro_meug_638, retro_meug_639, retro_meug_660, retro_meug_68, retro_meug_736, retro_meug_737, retro_meug_832, retro_meug_861, retro_meug_867, retro_meug_870, retro_meug_891, retro_meug_916, retro_meug_927, retro_meug_971, retro_meug_980, retro_meug_981,
Macaca mulatta ENSMMUG000000310242 retrocopies
retro_mmul_1037, retro_mmul_587,
Monodelphis domestica ENSMODG000000065222 retrocopies
retro_mdom_161, retro_mdom_206,
Mus musculus ENSMUSG0000006322914 retrocopies
retro_mmus_1044, retro_mmus_1300, retro_mmus_1514, retro_mmus_1608, retro_mmus_1753, retro_mmus_1887, retro_mmus_1889, retro_mmus_1925, retro_mmus_2078, retro_mmus_2592, retro_mmus_2885, retro_mmus_3150, retro_mmus_3694, retro_mmus_497,
Nomascus leucogenys ENSNLEG000000177674 retrocopies
retro_nleu_1037, retro_nleu_1303, retro_nleu_1766, retro_nleu_820,
Oryctolagus cuniculus ENSOCUG000000159396 retrocopies
retro_ocun_1597, retro_ocun_1817, retro_ocun_246, retro_ocun_338, retro_ocun_574, retro_ocun_746,
Pongo abelii ENSPPYG000000034375 retrocopies
retro_pabe_2002, retro_pabe_2039, retro_pabe_2423, retro_pabe_3407, retro_pabe_364,
Pan troglodytes ENSPTRG000000034215 retrocopies
retro_ptro_1540, retro_ptro_1618, retro_ptro_2039, retro_ptro_259, retro_ptro_2875,
Rattus norvegicus ENSRNOG0000001300917 retrocopies
retro_rnor_1131, retro_rnor_1336, retro_rnor_1738, retro_rnor_1769, retro_rnor_1881, retro_rnor_2146, retro_rnor_2377, retro_rnor_2560, retro_rnor_2830, retro_rnor_2950, retro_rnor_2957, retro_rnor_2984, retro_rnor_490, retro_rnor_491, retro_rnor_563, retro_rnor_578, retro_rnor_843,
Sorex araneus ENSSARG000000012241 retrocopy
retro_sara_657,
Sarcophilus harrisii ENSSHAG000000157761 retrocopy
retro_shar_814,
Sus scrofa ENSSSCG000000133661 retrocopy
retro_sscr_12,
Tarsius syrichta ENSTSYG000000080624 retrocopies
retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,
Tursiops truncatus ENSTTRG000000137562 retrocopies
retro_ttru_1269, retro_ttru_1802,
Vicugna pacos ENSVPAG000000102155 retrocopies
retro_vpac_175, retro_vpac_222, retro_vpac_237, retro_vpac_629, retro_vpac_79,

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 = 0.63 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .30 RPM
CEU_NA11843 0 .17 RPM
CEU_NA11930 0 .52 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .49 RPM
CEU_NA12751 0 .32 RPM
CEU_NA12760 0 .45 RPM
CEU_NA12827 0 .38 RPM
CEU_NA12872 0 .24 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .63 RPM
FIN_HG00277 0 .41 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .19 RPM
FIN_HG00338 0 .23 RPM
FIN_HG00349 0 .34 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .33 RPM
FIN_HG00378 0 .30 RPM
GBR_HG00099 0 .23 RPM
GBR_HG00111 0 .28 RPM
GBR_HG00114 0 .21 RPM
GBR_HG00119 0 .26 RPM
GBR_HG00131 0 .43 RPM
GBR_HG00133 0 .22 RPM
GBR_HG00134 0 .31 RPM
GBR_HG00137 0 .41 RPM
GBR_HG00142 0 .33 RPM
GBR_HG00143 0 .35 RPM
TSI_NA20512 0 .23 RPM
TSI_NA20513 0 .46 RPM
TSI_NA20518 0 .42 RPM
TSI_NA20532 0 .37 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .35 RPM
TSI_NA20765 0 .17 RPM
TSI_NA20771 0 .28 RPM
TSI_NA20786 0 .44 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .47 RPM
YRI_NA18907 0 .24 RPM
YRI_NA18916 0 .27 RPM
YRI_NA19093 0 .18 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .25 RPM
YRI_NA19213 0 .53 RPM
YRI_NA19214 0 .34 RPM
YRI_NA19223 0 .20 RPM

Indel association:

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



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