RetrogeneDB ID:

retro_pabe_1738

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1_random:720242..721204(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHB
Ensembl ID:ENSPPYG00000004356
Aliases:None
Description:lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]


Retrocopy-Parental alignment summary:






>retro_pabe_1738
ATGGCAACTCTTAAGGAAAAACTCATTGCACCAGTTGTAGAAGAGGCAACAGTCCCAGACAATAAGATCACTGTACTGGG
TGTTGGACAAATGGGTGTGGTGTGTGCTATCAGCATCTGGAAAAGTCTTTGGTTGATGAACTTCTTCTTGTGGATGTTTT
GGAACACGAGCTTAAAGGAGAAATGATGGATCAATCTGCAGATAGGAGTATATTTCCTCAGACACCTAAAATTGTGGCAG
ATAAAGATTATTCTATGACTGCCAATTAAAAGATTGTAGCGGTAACTGCAGGAGTCCATCAGCAAGAGGGGGAGAGTCGT
CTCAATCTGGTACAGAGAAATGTTAATGCCTTCAAATCTGTTGTTTCTCAGATCATTAAGTACAGTTCTAATTACATCAT
AATTGTGATTTCCAACCCATTGGCCGTTCTTACCTATGTTACCTGGAAACTAAGTGGATTACCCAAGCACCTTGTGATTG
GAAGTGGGTATAATTTGGATTCTGCTAGATTTTGCCACCTTGTGGCTGAAAAACTTGGCATTCATCTCGGCAGCTGCCAT
GGATGGATTTTGGGAGAACATGGTAATTCAAGTGTTGTTGTTCAGAGTGGTGTGAACATGGCAGGTGCTTCTCTCCAGGA
ATTGAATCCAGAAATGGGAACCAACAATGATCGTGAAACTTGGAAGGAAGTGCGTAAGATGGTGGTTGAAAGTGCCTATG
AGGTCAACAAGCCAAAAGGATATACCAACTGGGCTACTAGATTAAGTGTAGCTGATCTTGTTGAATCCATGTTGAAAAAT
CTATCCAGGATTCATCCAGAATGAACAATGATGAAGGGGATGAAGGGCATTGAGAATGAAGTCTTCCAGAGCCTTCCATG
TATCCTCAATACTCGGGAATTAACCAGCATTATCAACCAGAAGCTAAAGGATGATGAGTTTGCTCAGCTCAAGAAAAGTG
CA

ORF - retro_pabe_1738 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.26 %
Parental protein coverage: 96.11 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISI-LGKSLADELALVDVLEDKLKGEMMDLQHG
MATLKEKLIAPV.EE.ATVP.NKITV.GVGQ.G..CAISI.L.KSL.DEL.LVDVLE..LKGEMMD....
RetrocopyMATLKEKLIAPVVEE-ATVPDNKITVLGVGQMGVVCAISI<LEKSLVDELLLVDVLEHELKGEMMDQSAD
Parental-SLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVS
.S.F.QTPKIVADKDYS.TAN.KIV.VTAGV.QQEGESRLNLVQRNVN.FK....QI.KYS...IIIV.S
RetrocopyRSIFPQTPKIVADKDYSMTAN*KIVAVTAGVHQQEGESRLNLVQRNVNAFKSVVSQIIKYSSNYIIIVIS
ParentalNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVA
NP...LTYVTWKLSGLPKH.VIGSG.NLDSARF..L.AEKLGIH..SCHGWILGEHG.SSV.V.SGVN.A
RetrocopyNPLAVLTYVTWKLSGLPKHLVIGSGYNLDSARFCHLVAEKLGIHLGSCHGWILGEHGNSSVVVQSGVNMA
ParentalGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMV
G.SLQELNPEMGT.ND.E.WKEV.KMVVESAYEV.K.KGYTNWA..LSVADL.ESMLKNLSRIHP..TM.
RetrocopyGASLQELNPEMGTNNDRETWKEVRKMVVESAYEVNKPKGYTNWATRLSVADLVESMLKNLSRIHPE*TMM
ParentalKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSA
KGM.GIENEVF.SLPCILN.R.LTS.INQKLKDDE.AQLKKSA
RetrocopyKGMKGIENEVFQSLPCILNTRELTSIINQKLKDDEFAQLKKSA

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 504 .36 RPM
SRP007412_cerebellum 0 .00 RPM 372 .22 RPM
SRP007412_heart 0 .03 RPM 1192 .91 RPM
SRP007412_kidney 0 .03 RPM 860 .49 RPM
SRP007412_liver 0 .00 RPM 33 .91 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1738 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1738 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1738 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161754 retrocopies
Canis familiaris ENSCAFG000000121959 retrocopies
Echinops telfairi ENSETEG000000199551 retrocopy
Felis catus ENSFCAG000000126391 retrocopy
Macropus eugenii ENSMEUG000000048251 retrocopy
Myotis lucifugus ENSMLUG000000121551 retrocopy
Macaca mulatta ENSMMUG000000026794 retrocopies
Monodelphis domestica ENSMODG000000177861 retrocopy
Mustela putorius furoENSMPUG000000001725 retrocopies
Pongo abelii ENSPPYG000000034352 retrocopies
Pongo abelii ENSPPYG000000034375 retrocopies
Pongo abelii ENSPPYG00000004356 3 retrocopies
retro_pabe_1738 , retro_pabe_1744, retro_pabe_3780,
Sus scrofa ENSSSCG000000005761 retrocopy
Tarsius syrichta ENSTSYG000000137597 retrocopies



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