RetrogeneDB ID:

retro_ecab_919

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:7:18522089..18523450(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000003454
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSECAG00000007371
Aliases:None
Description:Glutamate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F6V4L4]


Retrocopy-Parental alignment summary:






>retro_ecab_919
GGCATCCTGCGGATCATCAAGCCTTGCAACCATGTGCTGAGCCTGTCCTTCCCCATCCGGCGCGATGATGGCTCCTAGGA
AGTCATCGAGGGCTACCGGGCCCAGCATAGCCAGCACCGCACGCCCTGCAAGGGAGGTATCCGTTACAGCACTGATGTGA
GTGTAGACGAAGTGAAGGCTTTGGCTTCTCTGATGACTTATAAGTGTGCAGTGGTTGATGTGCCATTTGGGGGTGCCAAA
GCTGGTGTTAAGATCAATCCCAAAAACTATACCGATAATGAATTGGAAAAGATCACGAGGAGGTTTACCATGGAGCTGGC
AAAGAAGGGCTTTATTGGTCCTGGCATTGATGTGCCTGCCCAGACATGAGCACGGGCGAGCGGGAGATGTCCTGGATTGC
TGACACCTATGCTAGCACCATAGGGCACTATGATATTAATGCCCACGCCTGTGTCACTGGGAAGCCCATCAGTCAGGGTG
GAATCTATGGGCGGATCTCTGCCACTGGCCGGGGTCTTTTCCATGGGATCGAGAACTTCATCAATGAAGCTTCTTACATG
AGCATTCTAGGAATGACGCCAGGGTTTGGAGATAAGACGTTTGTCGTTCAGGGGTTTGGTAACGTGGGCCTGCACTCTAT
GAGATACTTACATCGTTTCGGTGCTAAATGTATTGCTGTTGGTGAATCCGATGGGAGCATATGGAATCCAGATGGTATTG
ACCCAAAAGAACTGGAAGACTTCAAATTGCAACATGGATCCATCCTGGGCTTCCCCAAGGCAAAGCCCTATGAAGGGAGC
ATCTTGGAGGCCGACTGTGACATCCTGATTCCTGCTGCCAGGGAGAAGCAGCTGACCAAGTCCAATGCACCGAGAGTCAA
AGCCAAGATCATTGCTGAAGGTGCCAATGGACCGACAACTCCGGAAGCCGATAAGATTTCCCTGGAGAGAAACATTATGG
TTATTCCCGATCTCTACCTGAACACCGGAGGGGTGGTGTCCTACTTTGAGTGGCTGAAGAATCTCAATCACGTCAGCTAC
GGCCGCCTGACCATCAAATACGAAAGGGATTCCAACTACCACTTGCTGATGTCTGTTCAAGAGAGTTTGGAAGGAAAATT
TGGAAAGCACGGTGGGACGATCCCCATTGTGCCCACGGCAGAGTTCCAAGACAGGATATCGGGTGCATCTGAGAAGGACA
TCGTGCACTCCTGCTTAGCTTACACCATGGAGCGCTCTGCCCAGCAAATCATGTGTCCGGCCATGAAGTACAACCTGAGG
TTGGACCTGAGGACGGCTGCCTACGTCAACGCCATCGAGAAAGTCTTCAAGGTGTACAATGAAGCTGGTGTGACCTTCAC
A

ORF - retro_ecab_919 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.49 %
Parental protein coverage: 90.26 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGILRIIK-ANHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCA
GILRIIK..NHVLSLSFPIRRDDGS.EVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCA
RetrocopyGILRIIKPCNHVLSLSFPIRRDDGS*EVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCA
ParentalVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPA-PDMSTGEREMSWIADTYAS
VVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPA.PDMSTGEREMSWIADTYAS
RetrocopyVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPA<PDMSTGEREMSWIADTYAS
ParentalTIGHYDINAHACVTGKPISQGGIHGRISATGRGLFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNV
TIGHYDINAHACVTGKPISQGGI.GRISATGRGLFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNV
RetrocopyTIGHYDINAHACVTGKPISQGGIYGRISATGRGLFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNV
ParentalGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILGFPKAKPYEGSILEADCDILIPA
GLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILGFPKAKPYEGSILEADCDILIPA
RetrocopyGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILGFPKAKPYEGSILEADCDILIPA
ParentalASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYG
A.EKQLTKSNAPRVKAKIIAEGANGPTTPEADKI.LERNIMVIPDLYLN.GGV.VSYFEWLKNLNHVSYG
RetrocopyAREKQLTKSNAPRVKAKIIAEGANGPTTPEADKISLERNIMVIPDLYLNTGGV-VSYFEWLKNLNHVSYG
ParentalRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIM
RLT.KYERDSNYHLLMSVQESLE.KFGKHGGTIPIVPTAEFQDRISGASEKDIVHS.LAYTMERSA.QIM
RetrocopyRLTIKYERDSNYHLLMSVQESLEGKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSCLAYTMERSAQQIM
ParentalRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTFT
..AMKYNL.LDLRTAAYVNAIEKVFKVYNEAGVTFT
RetrocopyCPAMKYNLRLDLRTAAYVNAIEKVFKVYNEAGVTFT

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
SRP021940_articular_cartilage 6 .49 RPM 78 .57 RPM
SRP021940_cerebellum 9 .04 RPM 182 .23 RPM
SRP021940_embryo 8 .82 RPM 119 .42 RPM
SRP021940_placental_villous 7 .36 RPM 83 .52 RPM
SRP021940_synovial_membrane 12 .35 RPM 120 .24 RPM
SRP021940_testis 0 .77 RPM 19 .50 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_919 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_919 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_919 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 ENSECAG00000007371 2 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 ENSPPYG000000028273 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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