RetrogeneDB ID:

retro_tbel_3327

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:scaffold_137391:84965..86013(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSTBEG00000002563
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PDHA1
Ensembl ID:ENSTBEG00000014313
Aliases:None
Description:pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]


Retrocopy-Parental alignment summary:






>retro_tbel_3327
ATGAGGAAGATGCTGGCCGCTGTCGTCTCCCGCGTGTTGTCGGGTGTTGCCCAGAAGCCCGCCCGCAGAGTGCTGGTGGC
ATCCTACAACTACTCAAAAGATGCCACCTTTGAAATCAAGAAATGCGATCTTTACCGGTTGGAGGAGGGCCCTCCGCTCA
CCACGGTGCTCACCAGGGAGGATGGGCTCAAATACTACCGGATGATGCAGGTGGTTCGCCGCATGGAGCTGAAGGCGGAC
CAGCTGTACAAGCAGAAGTTCATCCGTGGCTTCTGTCACTTGTGCGACGGCCAGGAGGCCTGCTGCGTGGGCCTCGAGGC
AGGTATAAACGCCTCAGACCATGTCATCACGTCCTATCGGGCTCACGGCATAAGCTATACTCGGGGGCTTTCGGTCCGAT
CCATTCTGGCAGAGCTGATGGGACGAAGAGGAGGGTGTGCGAAAGGAAAAGGAGGGTCGATGCACATGTATGCCAAGAAC
TTCTACGGGGGCAATGGCATTGTGGGCGCCCAGGGCCCCTTGGGTGCTGGGGTTGCCCTGGCCTGTAAATATTTGGGAAA
CAGTGAAGTCTGCTTGACCTTATATGGGGATGGCGCTGCCAATCAGGGGCAGATAGCTGAAGCTTACAACATGGCAGCTT
TGTGGAAATTACCCTGTATTTTTGTTTGTGAGAATAACCTCTACGGGATGGGAACATCTGCTGATAGGGCTGCGGCCAGC
ACTGACTACTACAAGAGGGGCAACTTTATCCCAGGGCTGCGGGTGGATGGCATGGACGTTCTGTGTGTTCGCGAGGCAAC
CAAATTTGCAGCCGACTACTGTAGATCTGGAAACGGGCCCATTCTGATGGAGCTGCAGACCTACCGTTATCATGGACACA
GCATGAGCGACCCCGGGGTCAGTTACCGGACCCGAGAAGAGGTTCAGAAGGTTCGAAGTAAGAGTGACCCTATAATGCTT
CTCCAAGAGAGAATGTAAACAGCCAGCTGCCAGTATGAAGAATAAAAGAATCGACGCTGATGTGAGGAAGAATGATGATG
CCGTTCAG

ORF - retro_tbel_3327 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.9 %
Parental protein coverage: 90. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMRKMLAAV-SRVLSGAAQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPATTVLTREDGLRYYRMMQ
MRKMLAAV.SRVLSG.AQKPA.RVLVAS.N...DATFEIKKCDL.RLEEGPP.TTVLTREDGL.YYRMMQ
RetrocopyMRKMLAAVVSRVLSGVAQKPARRVLVASYNYSKDATFEIKKCDLYRLEEGPPLTTVLTREDGLKYYRMMQ
ParentalTVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVRQILAELT
.VRRMELKADQLYKQK.IRGFCHLCDGQEACCVGLEAGIN..DH.IT.YRAHG...TRGLSVR.ILAEL.
RetrocopyVVRRMELKADQLYKQKFIRGFCHLCDGQEACCVGLEAGINASDHVITSYRAHGISYTRGLSVRSILAELM
ParentalGRKGGCARGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYN
GR.GGCA.GKGGSMHMYAKNFYGGNGIVGAQ.PLGAG.ALACKY.G..EVCLTLYGDGAANQGQI.EAYN
RetrocopyGRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQGPLGAGVALACKYLGNSEVCLTLYGDGAANQGQIAEAYN
ParentalMAALWKLPCSFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGP
MAALWKLPC.F.CENN.YGMGTS..RAAASTDYYKRG.FIPGLRVDGMD.LCVREAT.FAA.YCRSG.GP
RetrocopyMAALWKLPCIFVCENNLYGMGTSADRAAASTDYYKRGNFIPGLRVDGMDVLCVREATKFAADYCRSGNGP
ParentalILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRM-VNSNLTSVEELKE-IDVEVRKEIE
ILMELQTYRYHGHSMSDPGVSYRTREE.Q.VRSKSDPIMLL..RM.VNS.L..V...KE.ID..VRK...
RetrocopyILMELQTYRYHGHSMSDPGVSYRTREEVQKVRSKSDPIMLLQERM<VNSQL-PV*RIKE<IDADVRKN-D
ParentalDAAQ
DA.Q
RetrocopyDAVQ

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






RNA-Seq - click to see more details

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tupaia belangeri was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_tbel_3327 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_3327 was not experimentally validated.

Retrocopy orthology:
Tupaia belangeri 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 22 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167301 retrocopy
retro_amel_400,
Bos taurus ENSBTAG000000198522 retrocopies
retro_btau_100, retro_btau_1807,
Callithrix jacchus ENSCJAG000000054962 retrocopies
retro_cjac_2414, retro_cjac_27,
Dipodomys ordii ENSDORG000000118481 retrocopy
retro_dord_35,
Equus caballus ENSECAG000000019641 retrocopy
retro_ecab_21,
Erinaceus europaeus ENSEEUG000000054851 retrocopy
retro_eeur_580,
Homo sapiens ENSG000001318281 retrocopy
retro_hsap_41,
Gorilla gorilla ENSGGOG000000135741 retrocopy
retro_ggor_59,
Myotis lucifugus ENSMLUG000000129322 retrocopies
retro_mluc_2363, retro_mluc_323,
Macaca mulatta ENSMMUG000000173361 retrocopy
retro_mmul_123,
Mustela putorius furoENSMPUG000000032691 retrocopy
retro_mputfur_812,
Mus musculus ENSMUSG000000312992 retrocopies
retro_mmus_63, retro_mmus_631,
Nomascus leucogenys ENSNLEG000000098051 retrocopy
retro_nleu_74,
Oryctolagus cuniculus ENSOCUG000000147481 retrocopy
retro_ocun_264,
Pongo abelii ENSPPYG000000201711 retrocopy
retro_pabe_129,
Pan troglodytes ENSPTRG000000217171 retrocopy
retro_ptro_79,
Pteropus vampyrus ENSPVAG000000054201 retrocopy
retro_pvam_1306,
Sarcophilus harrisii ENSSHAG000000153751 retrocopy
retro_shar_84,
Sus scrofa ENSSSCG000000236432 retrocopies
retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus ENSSTOG000000154331 retrocopy
retro_itri_1529,
Tupaia belangeri ENSTBEG00000014313 1 retrocopy
retro_tbel_3327 ,
Tursiops truncatus ENSTTRG000000006601 retrocopy
retro_ttru_1427,


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