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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTGAATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagtttgcaatccacatccttggtcacttttgcaagcatatgaattttatctttggtataattcagttgttctaattggccaaattcag

Basic information

species Zea mays
transcript GRMZM2G574782_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g29370.1 (Oryza sativa), 5'ss of exon 8
TGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTGAATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagtttgcaatccacatccttggtcacttttgcaagcatatgaattttatctttggtataattcagttgttctaattggccaaattcag
||| || | || ||||||||||||||||||| |||| ||||| ||||||||||| ||||||||||||||| ||||||| || || ||||||||||| ||||||| |||||       |||||| |||  ||  |  |||||||||||   | || |||||| |  | |||||   || ||||  || || | |||
TGACGATGCTGACAAAGAAGAGGTTATCAATGCATTAGTTGCTAATGTTGAATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt-------ccacattctttttcggtgctgcaagcatattcctgtt-tctttgatggatttcagcatttttaat--gcaaattccag
















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|5915132|gb|AW052773.1|AW052773
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|6031340|gb|AW076197.1|AW076197
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|91876904|gb|EB406861.1|EB406861
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|26457260|gb|CA828843.1|CA828843
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|32830978|gb|CD970656.1|CD970656
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|211338342|gb|FL476140.1|FL476140
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|13515715|gb|BG517991.1|BG517991
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATA-TTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|32828287|gb|CD967965.1|CD967965
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|21390180|gb|BQ528229.1|BQ528229
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGGC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|1366579|gb|W59841.1|W59841
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|7216517|gb|AW562639.1|AW562639
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|60339607|gb|DN206580.1|DN206580
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|78544664|gb|DV622162.1|DV622162
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|21809577|gb|BQ667895.1|BQ667895
EST:     CGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: CGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|32858009|gb|CD997690.1|CD997690
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|7304515|gb|AW600454.1|AW600454
EST:     CATCATTGAAACAACTTCAG                         GGTCAT-TTTGGAGGGATTGG-TTTCAAAAGAAAGAGCTCCAGGGAGTTGT
genomic: CATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGA-GGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGT
EST: gi|78021868|gb|DV490255.1|DV490255
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|24766702|gb|CA401849.1|CA401849
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|31355926|gb|CD440283.1|CD440283
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|32830644|gb|CD970322.1|CD970322
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|60399186|gb|DN232000.1|DN232000
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|31356801|gb|CD441158.1|CD441158
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|148938307|gb|EC882614.2|EC882614
EST:     TGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTGGTC
genomic: TGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|5915112|gb|AW052753.1|AW052753
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|32831486|gb|CD971164.1|CD971164
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|148939492|gb|EC884072.2|EC884072
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|5343257|gb|AI795562.1|AI795562
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
EST: gi|60356489|gb|DN223462.1|DN223462
EST:     AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAG                         GGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC
genomic: AATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 282

TGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTGAATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTCTTTGAGGATGTTCCTGTGGCGCTAAAGAACTGGCATGCTAGTGGCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 419

TGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTGAATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTCTTTGAGGATGTTCCTGTGGCGCTAAAGAACTGGCATGCTAGTGGCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 818

TGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTGAATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTCTTTGAGGATGTTCCTGTGGCGCTAAAGAACTGGCATGCTAGTGGCATAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 177

TGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTGAATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagt ... ccaaattcagGGTCATATTTGGAGGATTGGATTTCAAAAGAAAGAGCTACAGGGAGTTGTCTTTGAGGATGTTCCTGTGGCGCTAAAGAACTGGCATGCTAGTGGCATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTGAATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagtttgcaatccacatccttggtcacttttgcaagcatatgaattttatctttggtataattcagttgttctaattggccaaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA