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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccccgtcccctttttccgagcggtctcgaatttgagacctctccttgcccccctagctagctcccattcatctcagtattccccgctgtttccattaactcgttttgattttttcgccgtgcacgactgtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC

Basic information

species Zea mays
transcript GRMZM2G009876_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 1
gtaagcccccgtcccctttttccga--gcggtctcgaatttgagacctctccttgccc--------ccctagctagctcccattcatctcagtattccccgctgtttccattaactcgt-------------------tttgattttttcg-------ccgtgcacgactgtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC
||||| |||| || |||| | ||    || | ||| ||  |||   | || | |||||        ||     |  |  |   ||||||||| |  | |   | ||||| ||  |||||                   |||  |||||| |        | || |||| | |||||||||||||||||||||||||| ||||| ||||||||||||||||||  |||||||||| |||| ||||||||||||||||| | ||| ||||||||||||| ||
gtaagtccccctcgccttctccccgccgccgcctccaacctgacctcactgcgtgcccagttcctcccgggattcaccgctgatcatctcagcacccgcgagtctttccgtttcctcgtcgttctcgctttttttttttttattttttttgagttttctcctggacgagt-tggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGC
















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|211153702|gb|FL418639.1|FL418639
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211143002|gb|FL390386.1|FL390386
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211516347|gb|FL407295.1|FL407295
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211452151|gb|FL396750.1|FL396750
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|101382315|gb|EB813213.1|EB813213
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|74232800|gb|DT640714.1|DT640714
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211129107|gb|FL371425.1|FL371425
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211527014|gb|FL385877.1|FL385877
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCTCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|101390908|gb|EB817389.1|EB817389
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|6918424|gb|AW399954.1|AW399954
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|67038385|gb|CO464715.1|CO464715
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|101392350|gb|EB818104.1|EB818104
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211049010|gb|FL423464.1|FL423464
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCTAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211533317|gb|FL400722.1|FL400722
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|148953095|gb|EE152575.2|EE152575
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|31350057|gb|CD434414.1|CD434414
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|29946118|gb|CB815988.1|CB815988
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211133673|gb|FL369483.1|FL369483
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCTAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211159863|gb|FL403892.1|FL403892
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|76015209|gb|DT942379.1|DT942379
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211223443|gb|FL382579.1|FL382579
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGC
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGC
EST: gi|60351247|gb|DN218220.1|DN218220
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|88757436|gb|DY541577.1|DY541577
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211113966|gb|FL427446.1|FL427446
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|149027253|gb|EE046450.2|EE046450
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211258671|gb|FL369172.1|FL369172
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCATCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211300841|gb|FL383944.1|FL383944
EST:     GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATG                         CCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: GCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTG

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), 49 (downstream exon)
Score: 292

GGCCGCCGCAGCTCTTACTACTGGTGCCCTAAACGCCGATATCCCTGTTCGCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

GGCCGCCGCAGCTCTTACTACTGGTGCCCTAAACGCCGATATCCCTGTTCGCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 311

GGCCGCCGCAGCTCTTACTACTGGTGCCCTAAACGCCGATATCCCTGTTCGCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GGCCGCCGCAGCTCTTACTACTGGTGCCCTAAACGCCGATATCCCTGTTCGCCTCCCTTTCCCCACCCAAAACCCCGGCCTTCAGGGTTCCGGCACCATGgtaagccccc ... gtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctgtttccattaactcgttttgattttttcgccgtgcacgactgtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC
                   ttttgatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcccccgtcccctttttccgagcggtctcgaatttgagacctctccttgcccccctagctagctcccattcatctcagtattccccgctgtttccattaactcgttttgattttttcgccgtgcacgactgtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA