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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgtcgatttaatctctcagttgacatgctgacattattgttgttgatctatctgactgagtataccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT

Basic information

species Zea mays
transcript GRMZM2G087144_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087144_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g35960.1 (Oryza sativa), 3'ss of exon 1
tactgtcgatttaatctctcagttgacatgctgacattat-tgttgttgatc--tatctgactgagtataccatttgctggaa-tatacccta-tatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT
        | ||| ||| |||||||  |||      |||| | || ||||||  |||||  ||   |   ||| || ||  || ||| |  || | |  || |||||||||  | || ||||||||||| || |||||||||||||||| |||||||||| |||| |||||  || ||||||| || |||||||| |||||||||
-----attagttagtctgtcagttggtatggcagtgttatcttttattgatccatatcttccttgttgctccactttctaaaactattctttaatcttctttcagGGGTGGAATAAAGTCTCCATGGTCTCGAAGGAAAAGAAAACGAGTACTTTCTCGTCAACAATGGGAAGGTCTGTTTTCTGCTAATGGGAAACTTCGTGAT

upper sequence: GRMZM2G087144_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G13850.1 (Glycine max), 3'ss of exon 1
tactgtcgatttaa-tctctcagttgacatgctgac-attat-tgttgttgatctatctgactgagtataccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT
| || ||  | ||| | ||| |  |||  ||||| | ||| | | || |  |  |  || ||      ||  |||   |  |||         | | || ||||||| |||||||||| |||||||| || |||||||||||||  |  ||  | | | | || ||| | || |||||| |   | ||||||   | || |||
tcctttcactctaaatttcttaaatgat-tgctgcctattctctattctaaaattgacttacaagcagtaatattgaat--aattcttttggcaaaatttcagGGGTCGTCTTAAATCACCATGGTCACGCAGGAAAAGAAAACATGTCCTAACACCTCAGCAATGGAAAAGCTTGTTTACCCAAGATGGGAGAATACGGGAT

upper sequence: GRMZM2G087144_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G41000.1 (Glycine max), 3'ss of exon 1
tactgtcgatttaatctctcagttgacatgctgacattattgttgttgatctatctgactgagta-taccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT
   |   ||||  | | |       ||| |    ||  |      || | |  |       || | ||  |||   |  | ||        | | || ||||||| |||||||||| |||||||| || |||||||||||||  |  ||| | | | | || ||| | ||  ||||| |     ||||||   | || |||
gtttccggattcgaacccatgaccaacaggtcaccaagacacaactttaccgctgcatacaagcagtaatattgaata-attacttttggcaaaatttcagGGGTCGTCTTAAATCACCATGGTCACGCAGGAAAAGAAAACATGTCCTTACACCTCAGCAATGGAAAAGCGTGTTTACCCAGGATGGGAGAATACGGGAT

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|50332287|gb|CO527413.1|CO527413
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|50325323|gb|CO520449.1|CO520449
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|148959376|gb|EC905424.2|EC905424
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211081607|gb|FL369112.1|FL369112
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211426207|gb|FL392504.1|FL392504
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGG
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGG
EST: gi|211076165|gb|FL369890.1|FL369890
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGATAAGA
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGA
EST: gi|211469235|gb|FL410783.1|FL410783
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCYTAAATCTCCATGGTCCCGGAGGAAAAGAA
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAA
EST: gi|211097332|gb|FL386847.1|FL386847
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|148964953|gb|EE015802.2|EE015802
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211328212|gb|FL409834.1|FL409834
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211397522|gb|FL373465.1|FL373465
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         NNGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211392710|gb|FL395249.1|FL395249
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211476313|gb|FL383250.1|FL383250
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAAGAAAAGAAA-CGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|149106092|gb|EE291756.2|EE291756
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|211082072|gb|FL392684.1|FL392684
EST:     CCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGNAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGGAAAGAAA-CGAGCACTTT
genomic: CCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGG-AGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTT
EST: gi|148981030|gb|EE027393.2|EE027393
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
EST: gi|148939166|gb|EC883612.2|EC883612
EST:     GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCG                         GGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC
genomic: GCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTC

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: 47 (upstream exon), 48 (downstream exon)
Score: 68

TCGCAGCGGCTGCGGCTGGGAGCGCGGTGGCTGTGGTGTCGGCTGCGGTGGCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

TCGCAGCGGCTGCGGCTGGGAGCGCGGTGGCTGTGGTGTCGGCTGCGGTGGCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT


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

TCGCAGCGGCTGCGGCTGGGAGCGCGGTGGCTGTGGTGTCGGCTGCGGTGGCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 33

TCGCAGCGGCTGCGGCTGGGAGCGCGGTGGCTGTGGTGTCGGCTGCGGTGGCCGCCTCGTCTTCTTCCTCGCCGGCGTCGTCCTCGCCGCACTCGGAGCGgtaggtttct ... atatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatctatctgactgagtataccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT
       atctgac  putative branch site (score: 33)
                                          tatatatttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgtcgatttaatctctcagttgacatgctgacattattgttgttgatctatctgactgagtataccatttgctggaatataccctatatatttacagGGGTGGTCTTAAATCTCCATGGTCCCGGAGGAAAAGAAAACGAGCACTTTCTCGTGAACAGTGGGAGAGTTTGTTTTCAGCAAATGGGAAGCTTCGTGAT

- - - - - - - - - - - - - - tgctgac
- - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgctg