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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGCTCGACGTCATGGAGCTCGACCTCTCGTCCATGGCCTCTGTCCGCGCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtattatgtttatattaattgttgcctgctttgctacctgggatgaattatgactcctaacgaatcactaattcagtcaggagaaacagctcgtac...

Basic information

species Zea mays
transcript GRMZM2G009940_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009940_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g39670.1 (Oryza sativa), 5'ss of exon 1
CCAAGCTCGACGTCATGGAGCTCGACCTCTCGTCCATGGCCTCTGTCCGCGCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtat--gtattatgtttatattaattgttgcctgctttgctacctgggatgaattatgactcctaacgaatcactaattcagtcaggagaaacagctcg-tac
||   |||||| ||||||||||||||||| | ||||||| ||| |||||||| ||||| ||| | |||  || || ||| ||||||||||| ||||| |||||   ||| |    ||  | |      | |    |     |  |    | | ||| |||    |       ||  |      | | |   ||  |||  | |
CCTCCCTCGACCTCATGGAGCTCGACCTCGCCTCCATGGACTCCGTCCGCGCCTTCGCCTCCGACTTCGCCGCCAAGGGCCTCCCCCTCAATATCCTCATgtactagtactcctctttcaatgccaagtacaaattccctcatttt---tcagttaggaccagcagtatcctacctacctgcactgcattcactactcactgc
















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|76280839|gb|DV020407.1|DV020407
EST:     GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|31909769|gb|CD651085.1|CD651085
EST:     GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|78106300|gb|DV524718.1|DV524718
EST:     GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|76021078|gb|DT948248.1|DT948248
EST:     CTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCCTCA-CATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: CTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCC-TCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|78084860|gb|DV513253.1|DV513253
EST:     GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|149082933|gb|EE172168.2|EE172168
EST:     GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|71438305|gb|DR819355.1|DR819355
EST:     GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|74244969|gb|DT652883.1|DT652883
EST:     CTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: CTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|60343084|gb|DN210057.1|DN210057
EST:     ACAGGGGTCTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: ACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
EST: gi|78105169|gb|DV523587.1|DV523587
EST:     GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTAT                         CAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT
genomic: GCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAAT

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), 46 (downstream exon)
Score: 129

CCAAGCTCGACGTCATGGAGCTCGACCTCTCGTCCATGGCCTCTGTCCGCGCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAATTGAGATGCAGTTTGCAACTAATCATGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 233

CCAAGCTCGACGTCATGGAGCTCGACCTCTCGTCCATGGCCTCTGTCCGCGCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAATTGAGATGCAGTTTGCAACTAATCATGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 262

CCAAGCTCGACGTCATGGAGCTCGACCTCTCGTCCATGGCCTCTGTCCGCGCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAATTGAGATGCAGTTTGCAACTAATCATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

CCAAGCTCGACGTCATGGAGCTCGACCTCTCGTCCATGGCCTCTGTCCGCGCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtatta ... ttgctggcagCAACAATGCAGGAGTAATGGCAATACCTTTTGCGCTTTCAAAGGATGGAATTGAGATGCAGTTTGCAACTAATCATGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGCTCGACGTCATGGAGCTCGACCTCTCGTCCATGGCCTCTGTCCGCGCTTTCGCGTCCCAATTCATCGACAGGGGTCTCCCCCTCAACATCCTTATgtatgtattatgtttatattaattgttgcctgctttgctacctgggatgaattatgactcctaacgaatcactaattcagtcaggagaaacagctcgtac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaaaca