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






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 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

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_1738 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

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
retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
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,
Echinops telfairi ENSETEG000000199551 retrocopy
retro_etel_850,
Felis catus ENSFCAG000000126391 retrocopy
retro_fcat_462,
Macropus eugenii ENSMEUG000000048251 retrocopy
retro_meug_311,
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,
Pongo abelii ENSPPYG000000034352 retrocopies
retro_pabe_203, retro_pabe_779,
Pongo abelii ENSPPYG000000034375 retrocopies
retro_pabe_2002, retro_pabe_2039, retro_pabe_2423, retro_pabe_3407, retro_pabe_364,
Pongo abelii ENSPPYG00000004356 3 retrocopies
retro_pabe_1738 , retro_pabe_1744, retro_pabe_3780,
Sus scrofa ENSSSCG000000005761 retrocopy
retro_sscr_37,
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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