RetrogeneDB ID:

retro_pabe_3109

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:7:148328716..148330389(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GLUD1
Ensembl ID:ENSPPYG00000002827
Aliases:None
Description:glutamate dehydrogenase 1 [Source:HGNC Symbol;Acc:4335]


Retrocopy-Parental alignment summary:






>retro_pabe_3109
ATGTACCGCTACGTGGGCGAAGCGCTGCTGCTGTCCCGGGCCGGGCGGCTGCCCTGGGCTCCGCGGCCACCGACTCGGCT
GGGTTGCTGGGCCGGGCCCGGGGACAGCCCGCCGCCGCCCCGGAGCCGGGGCTCGCATTGGCCGCCCGGCGCCACTACAG
CGACGCGGTGGCCGACCGCGAGGACGACCCCAACTTCCTCAAGATGGTGGAGGGCTTCTTCTATCGCGGCGCCAGCATCG
TGGAGGACAAGCTGGTGGAGGACCTGAGGACCCGGGAGAGCGAGGAGCAGAAGCGGAACCGGGTGCGCGGCATCCTGCGG
ATCATCAAGCCCTGCAACCATGTGCTGAGTCTCTCCTTCCCCATCCGGCGCGACGACGGCTCCTGGGAGGTCATCTAAGG
CTACCGGGCCCAGCACAGCCAGCACCGCACACCCTGCAAGGGAGGTATCCGTTACAGCACTGATGTGAGTGTAGATGAAG
TAAAAACTTTGGCTTCTCTGGTGACATACAAGTGTGCAGTGGTTGATGTGCCGTTTGGGGGTGCTAAAGCTGGTGTTAAG
ATCAATCCCAAGAACTATACCGATAATGAATTGGAAAAGATCACAAGGAGGTTCACCATGGAACTAGCAAAGAAGGGCTT
TATTGGTCCTGGCATTGATGTGCCTGCTCCAGACATGAGCACAGGTGAGCGGGAGATGTCCTGGATCGCTGATACCTATG
TCAGCACCATAGGGCACTACGATATTAATGCACACGCCTGTGTTACTGGTAAACCCATCAGCCAAGAGGGCGTGCATGGA
CGCATCTCTGCTACTGGCCGTGGTGTCTTCCATAGGATTGAAAACTTCATCAGTGAAGCTTCTTACATGAGCATTTTAGG
AATGACACCAGGGTTTGGAGATAAAACATTTGTTGTTCAGGGATTTGGTAATGTGGGCCTACACTCTATGAGATATTTAC
ATCGTTTTGGTGCTAAGTGTATTGCTGTTGGTGAGTCTGATGGGAGTATATGGAATCCAGATGGTATTGACCTAAAGGAA
CTGGAAGACTTCAGATTGCAACATGGGTCCATTCTGGGCTTCCCCAAGGCAAAGCCCTATGAAGGAAGCATCTTGGAGGC
CGACTGTGACATACTGATCCCGGCTGCCGGTGAGAAGCAGTTGACCAAATCCAGCGCAGCCAGAGTCAAAGCCAAGATCA
TTGCTGAAGGTGCCAACGGGCCAATCACTCCAGAAGCTGACAAGGTCTTCCTGGAGAGAAACATTATGGTTATTCCAGAT
CTCTACTTGAATGCTGGAGGAGTGACAGTATCTTACTTTGAGTGGCTGAAGAATCTAAATCATGTCAGCTATGGCCGTTT
GACCTTCAAATATGAAAGGGATCCTAACTACCACTTGCTCATGTCTGTTCAAGAGAGTTTAGAAAGAAAATTTGGAAAGC
ACGGTGGAACTATTCCCATTGTACCCACAGCAGAGTTCCGAGACAGGATATCGGGTGCATCTGAGAAAGACATCATGCAC
TCTGGCTTGGCGTACACAATGGAGCATTCTTCCAGGCAAATTATGCGCACACACATGAAGTATAACCTGGGATTGGACCT
CAGAACAGCTGCCTATGTCAATGCCATTGAGAAAGTCTTCAAAGTGTACAGTGAAGCTGGTGTGAGCTTCACA

ORF - retro_pabe_3109 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.1 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMYRYLGEALLLSRAG-PAALGSASADSAALLGRARGQPAAAPQPGLALAARRHYSEAVADREDDPNFFKM
MYRY.GEALLLSRAG..AALGSA..DSA.LLGRARGQPAAAP.PGLALAARRHYS.AVADREDDPNF.KM
RetrocopyMYRYVGEALLLSRAG<AAALGSAATDSAGLLGRARGQPAAAPEPGLALAARRHYSDAVADREDDPNFLKM
ParentalVEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQH
VEGFF.RGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVI.GYRAQH
RetrocopyVEGFFYRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVI*GYRAQH
ParentalSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMEL
SQHRTPCKGGIRYSTDVSVDEVK.LASL.TYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMEL
RetrocopySQHRTPCKGGIRYSTDVSVDEVKTLASLVTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMEL
ParentalAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHG
AKKGFIGPGIDVPAPDMSTGEREMSWIADTY.STIGHYDINAHACVTGKPISQ.G.HGRISATGRGVFH.
RetrocopyAKKGFIGPGIDVPAPDMSTGEREMSWIADTYVSTIGHYDINAHACVTGKPISQEGVHGRISATGRGVFHR
ParentalIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELE
IENFI.EASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGID.KELE
RetrocopyIENFISEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDLKELE
ParentalDFKLQHGSILGFPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLE
DF.LQHGSILGFPKAKPYEGSILEADCDILIPAA.EKQLTKS.A.RVKAKIIAEGANGP.TPEADK.FLE
RetrocopyDFRLQHGSILGFPKAKPYEGSILEADCDILIPAAGEKQLTKSSAARVKAKIIAEGANGPITPEADKVFLE
ParentalRNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVP
RNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERD.NYHLLMSVQESLERKFGKHGGTIPIVP
RetrocopyRNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDPNYHLLMSVQESLERKFGKHGGTIPIVP
ParentalTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTFT
TAEF.DRISGASEKDI.HSGLAYTME.S.RQIMRT.MKYNLGLDLRTAAYVNAIEKVFKVY.EAGV.FT
RetrocopyTAEFRDRISGASEKDIMHSGLAYTMEHSSRQIMRTHMKYNLGLDLRTAAYVNAIEKVFKVYSEAGVSFT

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 .11 RPM 112 .24 RPM
SRP007412_cerebellum 0 .00 RPM 77 .34 RPM
SRP007412_heart 0 .00 RPM 38 .26 RPM
SRP007412_kidney 0 .03 RPM 142 .63 RPM
SRP007412_liver 0 .15 RPM 303 .14 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_3109 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3109 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3109 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000075402 retrocopies
retro_btau_1413, retro_btau_1741,
Canis familiaris ENSCAFG000000160951 retrocopy
retro_cfam_747,
Choloepus hoffmanni ENSCHOG000000011011 retrocopy
retro_chof_2002,
Callithrix jacchus ENSCJAG000000116331 retrocopy
retro_cjac_2830,
Dipodomys ordii ENSDORG000000097671 retrocopy
retro_dord_400,
Equus caballus ENSECAG000000073712 retrocopies
retro_ecab_886, retro_ecab_919,
Echinops telfairi ENSETEG000000196382 retrocopies
retro_etel_141, retro_etel_2024,
Homo sapiens ENSG000001486721 retrocopy
retro_hsap_31,
Gorilla gorilla ENSGGOG000000157701 retrocopy
retro_ggor_2954,
Loxodonta africana ENSLAFG000000120591 retrocopy
retro_lafr_504,
Microcebus murinus ENSMICG000000165261 retrocopy
retro_mmur_524,
Monodelphis domestica ENSMODG000000027561 retrocopy
retro_mdom_124,
Nomascus leucogenys ENSNLEG000000116581 retrocopy
retro_nleu_36,
Otolemur garnettii ENSOGAG000000036411 retrocopy
retro_ogar_2757,
Procavia capensis ENSPCAG000000086621 retrocopy
retro_pcap_11,
Pongo abelii ENSPPYG00000002827 3 retrocopies
retro_pabe_3109 , retro_pabe_3213, retro_pabe_79,
Pan troglodytes ENSPTRG000000027114 retrocopies
retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus ENSSTOG000000128431 retrocopy
retro_itri_737,
Tarsius syrichta ENSTSYG000000015781 retrocopy
retro_tsyr_313,
Tursiops truncatus ENSTTRG000000081451 retrocopy
retro_ttru_950,


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