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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaagttgcagctaaatctcgccccagctaattttttttctgggtccgccactgataactgtatacattcttgtggcggtgatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG

Basic information

species Zea mays
transcript GRMZM2G069008_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069008_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 5
tttaagttgcagctaaatctcgccccagctaattttttttctgggtccgccactgataactgtatacattcttgtggcggt-gatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG
 ||     | ||   ||      | ||       |||        | | | | |  |   |     || |    || |  | | | | |   |  |  ||||| ||||| |||| ||||||||| ||||| | |||||| ||||||||||| || ||  | || |||||  |||||||    || ||  | || || || 
attgtagagaagtcgaagtataactcaaaaggagtttgacaaactttctcgatttgtgttttgcgccagttacatgacttttgcttcgtggata-tatcagGTCGAAGAGGAGATTGGTATAAAACTGAAAAAAGAAGATATGGTTGATCTCACTGCTTTTCTTGACCCATCTACTGGTTACCGGATCTTCCCTTCTCCT
















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|78087423|gb|DV515816.1|DV515816
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|15215527|gb|BI431332.1|BI431332
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|148991429|gb|EE032931.2|EE032931
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|45847993|gb|CN071936.1|CN071936
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|149074764|gb|EE163194.2|EE163194
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|148942502|gb|EC887517.2|EC887517
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|91054277|gb|EB164695.1|EB164695
EST:     GGATGCTAGATGACGAAAAAGGTGACTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|29544119|gb|CB604499.1|CB604499
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|149096585|gb|EE182343.2|EE182343
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|149111714|gb|EE190861.2|EE190861
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|78082236|gb|DV510648.1|DV510648
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|113703128|gb|EE680632.1|EE680632
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|29543762|gb|CB604142.1|CB604142
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
EST: gi|31355362|gb|CD439719.1|CD439719
EST:     GGATGCTAGATGACGAAAAAGGTGATTTTGTTGTTTTTTCAGTCCGTGAG                         GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT
genomic: GGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 137

GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 169

GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 118

GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 154

GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAGgttagtatct ... ttgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgccactgataactgtatacattcttgtggcggtgatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG
                 tatacatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaagttgcagctaaatctcgccccagctaattttttttctgggtccgccactgataactgtatacattcttgtggcggtgatccttaattgctggcagGTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG