RetrogeneDB ID:

retro_pabe_3407

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:9:47378049..47379124(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000019210
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHA
Ensembl ID:ENSPPYG00000003437
Aliases:None
Description:L-lactate dehydrogenase A chain [Source:RefSeq peptide;Acc:NP_001126782]


Retrocopy-Parental alignment summary:






>retro_pabe_3407
GCGGATTCTGGATCTCATTGCCACGTGCCCCGACGACCGCCCGATGTGCATTCCCGATTCCTTTTGGTTCCAAGTCCAAT
ATGGCAACTCTCAAGGATCAGCTGATTCATAATCTTCTAAAGGAAGAACAGACCCCCCAGAATAAGATTACAGTTGTTGG
GGTTGGTGCTGTTGGCATGGCCTGTGCCATCAGTATCTTAATGAAGGACTTGGCAGATGAACTTGATCTTGTTGATGCCA
TCAAAGACAAATTGAAGGGAGAGATGATGGATCTCCAACATGGCAGCCTTTTCCTTAGAGCACCAAAGATTGTCTCTGGC
AAAGACTATAATATACCTGTAAACTCCAAACTGGTCATTATCACGGCTGGGACATGTCAGCAAGAGGGAGAAAGCTGTCT
TAATTTGGTCCAGCGTAACGTGAACATCTTTAAATTCATCATTCTTAATGTTGTAAAATACAGCCTGAACTGCAAGTTGC
TTATTGTTTCAAATCCAGTGGATATCTTGACCTATGTGGCTTGGAAGATATGTGGTTTTCGCAAAAACTGTGTTATTGGA
AGTGGTTGCAATCTGGATTCAGCCCGATTCCATTACCTGATGGGGGAAAGACTGGGAGTTCACCCATTAAGCTGTCATGG
GTGGGTCCTTGGGGAACATGGAGATTCCAGTGTGCCTGTATGGAGTAGAATGAATGTTGCTGGTGTCTCCCTGAAGACTC
CGCACCCAGATTTAGAGACTGATAAAGATAAGGAACAGTGGAAAGAGGTTCACAAACAAGTGGTTGAGAATGCTTATGAG
GTGATCAAACTCAAAGGCTACACATCCTGGGCCATTGGACTCTCTGTAGCAGATTTGGCAGAGAGTATAATGAAGAATCT
TAGGCAGGTGCACCCAGTTTTCACCATGATTAAGGGTCTCTATGGAATAAAGGATGATGTCTTCCTTAGGGTTCCTTGCA
TTTTGGGACAGAATGGAATCTCAGACCTTGTGAAGGTGACTCTGACTCCTGAGGAAGAGCCTGTTTGAAGAAGAGTGCAG
ATACACTTTGGGGGATCCAAAAAGAGCTGCAATTT

ORF - retro_pabe_3407 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.69 %
Parental protein coverage: 75.42 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalADSGSHCHAH-PTTARRAFPIPFGSKSNMATLKDQLIHNLLKEEQTPQNKITVVGVGAVGMACAISILMK
ADSGSHCH...PTTAR.AFPIPFGSKSNMATLKDQLIHNLLKEEQTPQNKITVVGVGAVGMACAISILMK
RetrocopyADSGSHCHVP<PTTARCAFPIPFGSKSNMATLKDQLIHNLLKEEQTPQNKITVVGVGAVGMACAISILMK
ParentalDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQR
DLADEL.LVD.I.DKLKGEMMDLQHGSLFLR.PKIVSGKDYN...NSKLVIITAG..QQEGES.LNLVQR
RetrocopyDLADELDLVDAIKDKLKGEMMDLQHGSLFLRAPKIVSGKDYNIPVNSKLVIITAGTCQQEGESCLNLVQR
ParentalNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHP
NVNIFKFII.NVVKYS.NCKLLIVSNPVDILTYVAWKI.GF.KN.VIGSGCNLDSARF.YLMGERLGVHP
RetrocopyNVNIFKFIILNVVKYSLNCKLLIVSNPVDILTYVAWKICGFRKNCVIGSGCNLDSARFHYLMGERLGVHP
ParentalLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAI
LSCHGWVLGEHGDSSVPVWS.MNVAGVSLKT.HPDL.TDKDKEQWKEVHKQVVE.AYEVIKLKGYTSWAI
RetrocopyLSCHGWVLGEHGDSSVPVWSRMNVAGVSLKTPHPDLETDKDKEQWKEVHKQVVENAYEVIKLKGYTSWAI
ParentalGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEE-ARLKKSAD
GLSVADLAESIMKNLR.VHPV.TMIKGLYGIKDDVFL.VPCILGQNGISDLVKVTLT.EEE.A.LKKSAD
RetrocopyGLSVADLAESIMKNLRQVHPVFTMIKGLYGIKDDVFLRVPCILGQNGISDLVKVTLTPEEE<ACLKKSAD
ParentalTLWGIQKELQF
TLWGIQKELQF
RetrocopyTLWGIQKELQF

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
SRP007412_brain_prefrontal_cortex 17 .75 RPM 88 .41 RPM
SRP007412_cerebellum 13 .01 RPM 85 .49 RPM
SRP007412_heart 6 .53 RPM 49 .76 RPM
SRP007412_kidney 6 .23 RPM 42 .20 RPM
SRP007412_liver 17 .99 RPM 139 .24 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_3407 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3407 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3407 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4231
Pan troglodytes retro_ptro_2875
Parental genes homology:
Parental genes homology involve 28 parental genes, and 226 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 ENSG000001343335 retrocopies
retro_hsap_2097, retro_hsap_2285, retro_hsap_3021, retro_hsap_323, retro_hsap_4231,
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 ENSPPYG000000034352 retrocopies
retro_pabe_203, retro_pabe_779,
Pongo abelii ENSPPYG00000003437 5 retrocopies
retro_pabe_2002, retro_pabe_2039, retro_pabe_2423, retro_pabe_3407 , retro_pabe_364,
Pongo abelii ENSPPYG000000043563 retrocopies
retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
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,


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