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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgctcagaaatactgggcataatatggtttcaagaattgcaattcatttgcttttgtgaaaacactcaatggcaattggccatgctctgaaatt...

Basic information

species Zea mays
transcript GRMZM5G841900_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 5'ss of exon 2
AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgctcagaaatactgggcat-aatatggttt-caagaattgc-aattcatttgcttttgtgaaaacactcaatggcaattggccatgctctgaaatt
|| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || || |||||||           |    | |   | ||  |     ||  ||  || |  || |||| |      | || |  | | | || |    | | |||    
AGGTCCACGGTGGAGGTGGTCGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATTGCGCGTgtaagatctatctctgagcaaaccgttggtttgactcgtgtgacctgtgaaattgttagcttattgttgtataccctgttg-attttgtgtggatgtgacg--
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211118858|gb|FL110173.1|FL110173
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|148935198|gb|EC879233.2|EC879233
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|60336704|gb|DN203677.1|DN203677
EST:     ACAAGGCCCAAGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102907|gb|FK962288.1|FK962288
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|148991615|gb|EE033149.2|EE033149
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118854|gb|FL110169.1|FL110169
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102910|gb|FK962291.1|FK962291
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|78180011|gb|DV550384.1|DV550384
EST:     CGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: CGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118860|gb|FL110175.1|FL110175
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|12046009|gb|BF728044.1|BF728044
EST:     CCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: CCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211326704|gb|FL445906.1|FL445906
EST:     GTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: GTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|32796285|gb|CD948521.1|CD948521
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118856|gb|FL110171.1|FL110171
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTYGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|60341943|gb|DN208916.1|DN208916
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118859|gb|FL110174.1|FL110174
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102909|gb|FK962290.1|FK962290
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|28873659|gb|CB329617.1|CB329617
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118857|gb|FL110172.1|FL110172
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|148965500|gb|EE016317.2|EE016317
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|6827420|gb|AW331063.1|AW331063
EST:     GCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: GCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102908|gb|FK962289.1|FK962289
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102903|gb|FK962284.1|FK962284
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|71439027|gb|DR820077.1|DR820077
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102902|gb|FK962283.1|FK962283
EST:     CAAGGCCCATGGAGCTGTGCCACAGCCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: CAAGGCCCATGGAGCTGTGCCGCAGCC-GGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|148935199|gb|EC879234.2|EC879234
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgctcagaaatactgggcataatatggtttcaagaattgcaattcatttgcttttgtgaaaacactcaatggcaattggccatgctctgaaatt

- - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - GGAGCT