RetrogeneDB ID:

retro_nleu_1303

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397288.1:21822368..21823238(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHA
Ensembl ID:ENSNLEG00000017767
Aliases:None
Description:lactate dehydrogenase A [Source:HGNC Symbol;Acc:6535]


Retrocopy-Parental alignment summary:






>retro_nleu_1303
AGTGCTGGAGCCGTTGCCACCAAGTCCAGGTCTCACTGCCACACGCCCCCGATACTTGCCTGACGTGCATTCCCAATTGC
TTTTGGTTCCAAGTCCAATATTGCAACTCTCAAGGATCAGCTGACTCATAATCTTCTAAAAGAAGAGCAGATCCCCCCAT
AAGATTACAGTTGTTGGGGTTTGTGCTGTTGCCATGATCTGTACCATCAGTATCTTAATGAAGGACTTGGCAGATGAACT
TGCTCTTGTTAATGTCATGGAAGACAAATTGAAGAGAGAGATAATGGATCTCCAACATGGCAGCCTTTTCCTTAGAACAC
CAAAGATTATCTCTGGCAAAGGCTATAATGTAACTGCAAACTCCAAGCTGGTCATTATCACGTCTGGGGCACATCAGCAA
GAGGGAGAAAGCCGTCTTAAATAGGACCAGCATAACATGAACATCTTTAAATTCATCATTCCTAATGTTGTAAAATACAG
CCCGAACTGCAAGTTGCTTATTGTTTCAAATCCAGTGGATATCTTGACCTATGCGGCTTGGAAGATAAGTGGCTTTCCCA
AAAACCGTGTTATTGGAAGTGGTTGCAGTCTGGATTCAGCCCAATTCGGTTACCTGATGGGGGAAAGCTGGGAGTTCACC
CATTAAGCTGTCATGGGCGGGTCCTTGGGGAACATGGAGATTCTAGTGTGCCTTTATGGAGTGGAGTGAATGTTGCTGGT
GTTTCCCTGAAGACTCTGCACTCACATTTAGGGACTGATACAGATAAGGAACAGTGGAAAGAGGTTCACAAGCAGGTGGT
TGAGAGTCCTTACAAGGTGATCAAACTGAAAGGCTACACATCCTAGGCCATTGGACTCTCCCCATTGGAC

ORF - retro_nleu_1303 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.25 %
Parental protein coverage: 68.47 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSAAAAAADSGSHCHAPQTTFRRAFPIPFGSKSNMATLKDQLIHNLLKEEQ-TPQNKITVVGVGAVGMACA
SA.A.A..S.SHCH.P.....RAFPI.FGSKSN.ATLKDQL.HNLLKEEQ..P..KITVVGV.AV.M.C.
RetrocopySAGAVATKSRSHCHTPPILA*RAFPIAFGSKSNIATLKDQLTHNLLKEEQ>SP-HKITVVGVCAVAMICT
ParentalISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESR
ISILMKDLADELALV.V.EDKLK.E.MDLQHGSLFLRTPKI.SGK.YNVTANSKLVIIT.GA.QQEGESR
RetrocopyISILMKDLADELALVNVMEDKLKREIMDLQHGSLFLRTPKIISGKGYNVTANSKLVIITSGAHQQEGESR
ParentalLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGE
L...Q.N.NIFKFIIPNVVKYSPNCKLLIVSNPVDILTY.AWKISGFPKNRVIGSGC.LDSA.F.YLMGE
RetrocopyLK*DQHNMNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYAAWKISGFPKNRVIGSGCSLDSAQFGYLMGE
Parental-RLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLK
..LGVHPLSCHG.VLGEHGDSSVP.WSG.NVAGVSLKTLH..LGTD.DKEQWKEVHKQVVES.Y.VIKLK
Retrocopy<KLGVHPLSCHGRVLGEHGDSSVPLWSGVNVAGVSLKTLHSHLGTDTDKEQWKEVHKQVVESPYKVIKLK
ParentalGYTSWAIGLSVAD
GYTS.AIGLS..D
RetrocopyGYTS*AIGLSPLD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Nomascus leucogenys was not studied using RNA-Seq expression data.
Nomascus leucogenys was not studied using ChIP-Seq data.
Nomascus leucogenys was not studied using EST data.
Nomascus leucogenys was not studied using FANTOM5 data.
retro_nleu_1303 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 27 parental genes, and 223 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178542 retrocopies
Bos taurus ENSBTAG000000086832 retrocopies
Choloepus hoffmanni ENSCHOG0000000997714 retrocopies
Callithrix jacchus ENSCJAG000000070941 retrocopy
Cavia porcellus ENSCPOG000000119262 retrocopies
Dasypus novemcinctus ENSDNOG0000001891511 retrocopies
Equus caballus ENSECAG000000206695 retrocopies
Echinops telfairi ENSETEG0000000750815 retrocopies
Homo sapiens ENSG000001343335 retrocopies
Gorilla gorilla ENSGGOG000000103503 retrocopies
Loxodonta africana ENSLAFG000000113071 retrocopy
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
Monodelphis domestica ENSMODG000000065222 retrocopies
Mus musculus ENSMUSG0000006322914 retrocopies
Nomascus leucogenys ENSNLEG00000017767 4 retrocopies
Nomascus leucogenys ENSNLEG000000177802 retrocopies
Oryctolagus cuniculus ENSOCUG000000159396 retrocopies
Pongo abelii ENSPPYG000000034375 retrocopies
Pan troglodytes ENSPTRG000000034215 retrocopies
Rattus norvegicus ENSRNOG0000001300917 retrocopies
Sorex araneus ENSSARG000000012241 retrocopy
Sarcophilus harrisii ENSSHAG000000157761 retrocopy
Sus scrofa ENSSSCG000000133661 retrocopy
Tarsius syrichta ENSTSYG000000080624 retrocopies
Tursiops truncatus ENSTTRG000000137562 retrocopies
Vicugna pacos ENSVPAG000000102155 retrocopies



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