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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttccctctattaaactttatctttgcaaccactgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG

Basic information

species Zea mays
transcript GRMZM2G431350_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G431350_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 3
gttattttccctctattaaactttatctttgcaac-cactgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG
|||||  ||   ||||| || | ||||||||     |    |||| || ||||  |  ||  |||    |  ||||||| || | | | |||||||  | |    ||||||||||| |  || |||||||| ||||||||||| ||| ||||| | |||||||||||||| ||||||||||||||||||||
gttatactcaacctatttaa-tgtatctttgtttttctaccttttattttgttttacatttatgtccctac-ctgattgcatgt-attctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG

upper sequence: GRMZM2G431350_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G02270.3 (Glycine max), 3'ss of exon 3
gttattttccctctattaaactttatctttgcaaccactgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG
||| |  ||   |    | | ||||| | ||   |   |     | | | ||  || |     | ||||  | | | ||   ||| ||  ||| |  ||||      |  |||  ||  || ||||| | |  |||||| ||||| |||||| | || ||||||||| | ||||||||||||||||| ||
gttgtggtcttacataaacaatttatatatgttccatgttcaagggtgtttttaatctatcactattaacacag-tagtccttga-tgattttactgtcttttcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATAGATGAAATTGTTGATGGCGG

upper sequence: GRMZM2G431350_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G13190.2 (Glycine max), 3'ss of exon 3
gttattttccctctattaa-actttatctttgcaaccactgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG----------------------
||| |  ||  | |||||| | ||||||| ||   |   |     | | | ||  || |     | ||||  | | | ||   ||| ||  ||| |   |||      | ||||  ||  || ||||| | |  |||||| ||||| |||||| | || ||||||||| ||||||||||||||||||| ||                      
gttgtaatct-tatattaacaatttatctatgtttcgtgttcaagggtgttttcaatctatcactattaacacag-tagtccttga-tgattttactgccttttcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATTGATGAAATTGTTGATGGCGGGTATGCTATATGCTATTCATAT

upper sequence: GRMZM2G431350_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G13190.3 (Glycine max), 3'ss of exon 3
gttattttccctctattaa-actttatctttgcaaccactgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG
||| |  ||  | |||||| | ||||||| ||   |   |     | | | ||  || |     | ||||  | | | ||   ||| ||  ||| |   |||      | ||||  ||  || ||||| | |  |||||| ||||| |||||| | || ||||||||| ||||||||||||||||||| ||
gttgtaatct-tatattaacaatttatctatgtttcgtgttcaagggtgttttcaatctatcactattaacacag-tagtccttga-tgattttactgccttttcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATTGATGAAATTGTTGATGGCGG

upper sequence: GRMZM2G431350_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G02270.2 (Glycine max), 3'ss of exon 3
gttattttccctctattaaactttatctttgcaaccactgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG----------------------
||| |  ||   |    | | ||||| | ||   |   |     | | | ||  || |     | ||||  | | | ||   ||| ||  ||| |  ||||      |  |||  ||  || ||||| | |  |||||| ||||| |||||| | || ||||||||| | ||||||||||||||||| ||                      
gttgtggtcttacataaacaatttatatatgttccatgttcaagggtgtttttaatctatcactattaacacag-tagtccttga-tgattttactgtcttttcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATAGATGAAATTGTTGATGGCGGGTATGCTATATGCTATTCATAT

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|30591255|gb|CD052281.1|CD052281
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|211420227|gb|FL011433.1|FL011433
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|32863613|gb|CF003295.1|CF003295
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|22819983|gb|BU500073.1|BU500073
EST:     TTAGCATCAGTTCTTGAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|211420230|gb|FL011436.1|FL011436
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGAT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGAT
EST: gi|22545780|gb|BU098154.1|BU098154
EST:     TTAGCATCAGTTCTTGAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|30591528|gb|CD052418.1|CD052418
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|211270446|gb|FL011426.1|FL011426
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|71302986|gb|DR787604.1|DR787604
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|6020321|gb|AW065249.1|AW065249
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|211270449|gb|FL011429.1|FL011429
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGC
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGC
EST: gi|211420231|gb|FL011437.1|FL011437
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|86468241|gb|DY234611.1|DY234611
EST:     TTAACATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|211420229|gb|FL011435.1|FL011435
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGAWGCTGTCGAACGACTTCTCAA                         AAACATGGTTGAC
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGAC
EST: gi|37622066|gb|CF675119.1|CF675119
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|211420226|gb|FL011432.1|FL011432
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|30591531|gb|CD052420.1|CD052420
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|32929387|gb|CF034199.1|CF034199
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|211477577|gb|FL100777.1|FL100777
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
EST: gi|33093855|gb|CF053849.1|CF053849
EST:     TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAA                         AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT
genomic: TTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATT

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), 48 (downstream exon)
Score: 160

AAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

AAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

AAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 127

AAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttcc ... gtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG
            tgctgat  putative branch site (score: 127)
                 attgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattttccctctattaaactttatctttgcaaccactgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG