RetrogeneDB ID:

retro_sscr_37

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:2:12622387..12623392(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000013171
Aliases:LDHB, LDH-B, LDH-H
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSSCG00000000576
Aliases:None
Description:L-lactate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F1SR05]


Retrocopy-Parental alignment summary:






>retro_sscr_37
ATGGCAACTCTTAAGGAAAAACTGATTGTACCAGTTGCAGAAGAAGAGACAACAATCCCAAACAATAAGATCACTGTAGT
GGGTGTTGGACAAGTCGGTATGGCATGTGCCATCAGCATTCTGGGAAAGTCTCTGACGGATGAGCTTGCTCTGGTGGATG
TTTTGGAAGATAAACTCAAAGGAGAAATAATGGATCTGCAGCACGGAAGCTTGTTCCTTCAGACACCCAAAATTGTGGCA
GATAAAGATTACTCTGTGACCGCCAATTCCAAGATTGTGGTGGTGACGGCAGGCGTTCGCCAGCAGGAGGGAGAGAGTCG
TCTCAATCTGGTGCAGAGGAACGTCAATGTCTTCAAGTTCATCATCCCTCAGATTGTCAAGTACAGTCCTGACTGCATCA
TAATTGTGGTTTCGAACCCAGTGGATATTCTCACATATGTTACCTGGAAACTAAGTGGATTACCCAAGCACCGTGTGATT
GGAAGTGGATGTAACCTGGATTCTGCAAGGTTTCGCTATCTTATGGCTGAAAAGCTTGGCGTTCATCCCAGCAGCTGCCA
CGGGTGGATTTTGGGAGAACATGGCGACTCAAGCGTGGCTGTGTGGAGTGGGGTGAATGTGGCAGGTGTGTCTCTCCAGG
AACTGAATCCAGAGATGGGAACGGACAATGATAGTGAAAATTGGAAAGAAGTGCATAAGATGGTGGTTGAAAGTGCCTAC
GAAGTCATCAAGCTGAAAGGCTACACCAACTGGGCAATTGGCTTAAGTGTGGCAGATCTTATTGAATCCATGTTGAAAAA
CCTATCCAGGATTCACCCAGTGTCAACAATGGTGCAGGGCATGTATGGCATTGAGAATGAGGTCTTCCTGAGCCTCCCAT
GTGTCCTGAATGCTCGCGGACTAACCAGTGTTATCAACCAGAAGCTGAAGGATGATGAGGTTGCCCAGCTCAAGAACAGT
GCTGACACTCTGTGGGGCATCCAGAAGGACCTGAAGGACCTGTGA

ORF - retro_sscr_37 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.3 %
Parental protein coverage: 96.14 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMATLKEKLIAPVAEEETTIPNNKITVVGVGQVGMACAISILGKSLTDELALVDVLEDKLKGEMMDLQHGS
MATLKEKLI.PVAEEETTIPNNKITVVGVGQVGMACAISILGKSLTDELALVDVLEDKLKGE.MDLQHGS
RetrocopyMATLKEKLIVPVAEEETTIPNNKITVVGVGQVGMACAISILGKSLTDELALVDVLEDKLKGEIMDLQHGS
ParentalLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP
LFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP
RetrocopyLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP
ParentalVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGVHPSSCHGWILGEHGDSSVAVWSGVNVAGV
VDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGVHPSSCHGWILGEHGDSSVAVWSGVNVAGV
RetrocopyVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGVHPSSCHGWILGEHGDSSVAVWSGVNVAGV
ParentalSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVQG
SLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVQG
RetrocopySLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVQG
ParentalMYGIENEVFLSLPCVLNARGLTSVINQKLKDLELVPLDNESQAI
MYGIENEVFLSLPCVLNARGLTSVINQKLKD.E...L.N.....
RetrocopyMYGIENEVFLSLPCVLNARGLTSVINQKLKDDEVAQLKNSADTL

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
SRP014902_placenta 8 .63 RPM 19 .11 RPM
SRP014902_testis 48 .52 RPM 119 .81 RPM
SRP018288_heart 381 .27 RPM 903 .47 RPM
SRP018288_kidney 167 .36 RPM 383 .78 RPM
SRP018288_liver 51 .17 RPM 134 .16 RPM
SRP018288_lung 40 .93 RPM 89 .61 RPM
SRP018856_adipose 537 .87 RPM 1805 .17 RPM
SRP035408_brain 85 .50 RPM 197 .30 RPM
SRP035408_liver 64 .17 RPM 189 .96 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_37 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_37 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_37 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 29 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161754 retrocopies
retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Bos taurus ENSBTAG000000196034 retrocopies
retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647,
Canis familiaris ENSCAFG000000121959 retrocopies
retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Choloepus hoffmanni ENSCHOG000000076581 retrocopy
retro_chof_1145,
Cavia porcellus ENSCPOG000000071381 retrocopy
retro_cpor_762,
Dasypus novemcinctus ENSDNOG000000136204 retrocopies
retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Echinops telfairi ENSETEG000000199551 retrocopy
retro_etel_850,
Felis catus ENSFCAG000000126391 retrocopy
retro_fcat_462,
Homo sapiens ENSG000001117161 retrocopy
retro_hsap_4863,
Gorilla gorilla ENSGGOG000000157581 retrocopy
retro_ggor_3033,
Loxodonta africana ENSLAFG000000009722 retrocopies
retro_lafr_197, retro_lafr_315,
Macropus eugenii ENSMEUG000000048251 retrocopy
retro_meug_311,
Microcebus murinus ENSMICG000000171832 retrocopies
retro_mmur_275, retro_mmur_300,
Myotis lucifugus ENSMLUG000000121551 retrocopy
retro_mluc_202,
Macaca mulatta ENSMMUG000000026794 retrocopies
retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica ENSMODG000000177861 retrocopy
retro_mdom_1484,
Mustela putorius furoENSMPUG000000001725 retrocopies
retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Mus musculus ENSMUSG000000302464 retrocopies
retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Oryctolagus cuniculus ENSOCUG000000220151 retrocopy
retro_ocun_805,
Otolemur garnettii ENSOGAG000000047639 retrocopies
retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pongo abelii ENSPPYG000000043563 retrocopies
retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
Pan troglodytes ENSPTRG000000047621 retrocopy
retro_ptro_3237,
Pteropus vampyrus ENSPVAG000000024623 retrocopies
retro_pvam_1487, retro_pvam_320, retro_pvam_673,
Rattus norvegicus ENSRNOG000000130003 retrocopies
retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Sorex araneus ENSSARG000000025651 retrocopy
retro_sara_713,
Sus scrofa ENSSSCG00000000576 1 retrocopy
retro_sscr_37 ,
Sus scrofa ENSSSCG000000133661 retrocopy
retro_sscr_12,
Ictidomys tridecemlineatus ENSSTOG000000220582 retrocopies
retro_itri_501, retro_itri_648,
Tarsius syrichta ENSTSYG000000137597 retrocopies
retro_tsyr_1130, retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,


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