RetrogeneDB ID:

retro_dnov_797

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_108768:914..1617(+)
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:ENSDNOG00000018915
Aliases:None
Description:lactate dehydrogenase A [Source:HGNC Symbol;Acc:6535]


Retrocopy-Parental alignment summary:






>retro_dnov_797
GACTATAGTGTGACTGCAAACTCCAAGCTGGTTATTATCACAGCTAGGGCACATCAGCAAGAGGGAGAAAGCCATCTTAA
TTTAGTCCAGTGTAATGTAAACATCTTTACATTCATCATTCCTAATGTTGTACAACACAGCCCGAATTTCAAGTTGTTTG
TTTTTTTCCAATCCAGTGGATATCTTGACCTATGTGGCTTGGAAACGAAGTGACTTTCCCAAAAGCAGTGTTATTGGAAG
TGGTTGCCATCTGGATACAGCCTGGTTCTGTTACCTAATGGGGGAGAAGCTGAGAGTTCACCCAATAAGCTGTTGTGGCT
GGGTCCTTAGGGAACATGGAGACTCTAGTGTGCCTGTGTGGAGTGGAGTGAATGTTGCTCGTGTCTCCTTGAAAAATCTG
CATCCTGAGTTAGGCACTGATGCAGATAAGGAACAGTGGAAAGAGATTTGCAAACAGGTGGTTGACAGTGTTTATGAGGC
GATCAAACTGAAAGGCTATACCTCCTGGGCCTTTGGGCTGTCTGTGGCAGATTTGGCAGAAAGTATAATGAGGAATCTTA
GGTGGATATATCTGATTTCCACCAGGATGAAGGGACACTATGGAATAAAAGAAGACATCTTCCTTAGTGTTCCTTGCATC
TTGGGACAAAACAGAATCTCAGATGTTGTCAAAGTGACTCTGACTCCTGAAGAAGAGTGCAGA

ORF - retro_dnov_797 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.3 %
Parental protein coverage: 71.69 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalNYSVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKL-LIVSNP-DILTYVAWKL
.YSVTANSKLVIITA.A.QQEGES.LNLVQ.NVNIF.FIIPNVV..SPN.KL.L..SNP.DILTYVAWK.
RetrocopyDYSVTANSKLVIITARAHQQEGESHLNLVQCNVNIFTFIIPNVVQHSPNFKL>LFFSNPVDILTYVAWKR
ParentalSGFPKNRVIGSGCNLDSARFRYLMGERLGVHPSSCHGWVLGEHGDSSVPVWSGMNVAGVSLKNLHPELGT
S.FPK..VIGSGC.LD.A.F.YLMGE.L.VHP.SC.GWVL.EHGDSSVPVWSG.NVA.VSLKNLHPELGT
RetrocopySDFPKSSVIGSGCHLDTAWFCYLMGEKLRVHPISCCGWVLREHGDSSVPVWSGVNVARVSLKNLHPELGT
ParentalDADKEQWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAETIMKNLRRVHPVSIMIKGLYGIKDENILS
DADKEQWKE..KQVVDS.YE.IKLKGYTSWA.GLSVADLAE.IM.NLR.....S...KG.YGIK....LS
RetrocopyDADKEQWKEICKQVVDSVYEAIKLKGYTSWAFGLSVADLAESIMRNLRWIYLISTRMKGHYGIKEDIFLS
ParentalVPCVLGQNGISDVVKVTLTPEEEGR
VPC.LGQN.ISDVVKVTLTPEEE.R
RetrocopyVPCILGQNRISDVVKVTLTPEEECR

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






(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
SRP012922_ascending_colon 0 .00 RPM 78 .95 RPM
SRP012922_cerebellum 0 .00 RPM 17 .73 RPM
SRP012922_heart 0 .00 RPM 17 .87 RPM
SRP012922_kidney 0 .00 RPM 29 .84 RPM
SRP012922_liver 0 .00 RPM 66 .10 RPM
SRP012922_lung 0 .00 RPM 22 .30 RPM
SRP012922_quadricep_muscle 0 .00 RPM 270 .18 RPM
SRP012922_spleen 0 .00 RPM 26 .55 RPM
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_797 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus 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 225 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 ENSDNOG000000136204 retrocopies
Dasypus novemcinctus ENSDNOG00000018915 11 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 ENSNLEG000000177674 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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