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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttctgacctctgattagtttacgcccttttggttttgttgttcatgtgcccctgttgttgatgatcacgtgccttgtgctgttgtag

Basic information

species Zea mays
transcript GRMZM2G009876_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 2
GCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttctgacctctgattagtttacgcccttttggtt---ttgttgttcatgtgcccctgttgttgatgatcacgtgccttgtgctgttgtag
||| ||||||||||||||||||  |||||||||| |||| ||||||||||||||||| | ||| ||||||||||||| ||| || | |||||||||  | ||| |   |||   | |  |       | ||  ||  |||   || || ||  || |   |||||| |||||  | || |  |||| |||| | ||
GCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGCGATCCAGGGATGCCCGGCAGgtgagagactg-tttatattccccccccccctcttctgttcaattttttttggtgcgtttctgttgctgatgcgcgcgcgt-ttgttctgtggcag
















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:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211143002|gb|FL390386.1|FL390386
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211516347|gb|FL407295.1|FL407295
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211452151|gb|FL396750.1|FL396750
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|101382315|gb|EB813213.1|EB813213
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|74232800|gb|DT640714.1|DT640714
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211129107|gb|FL371425.1|FL371425
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCCCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211527014|gb|FL385877.1|FL385877
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|101390908|gb|EB817389.1|EB817389
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|6918424|gb|AW399954.1|AW399954
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|67038385|gb|CO464715.1|CO464715
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|101392350|gb|EB818104.1|EB818104
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211049010|gb|FL423464.1|FL423464
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAAAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211533317|gb|FL400722.1|FL400722
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|148953095|gb|EE152575.2|EE152575
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|31350057|gb|CD434414.1|CD434414
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|29946118|gb|CB815988.1|CB815988
EST:     GC-AGCGCGAGGCCCGCGAGGTGCAC-GGCGCTCG-AGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAG-AG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211133673|gb|FL369483.1|FL369483
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAAAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211159863|gb|FL403892.1|FL403892
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|76015209|gb|DT942379.1|DT942379
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|60351247|gb|DN218220.1|DN218220
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|88757436|gb|DY541577.1|DY541577
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211113966|gb|FL427446.1|FL427446
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|149027253|gb|EE046450.2|EE046450
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211258671|gb|FL369172.1|FL369172
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211300841|gb|FL383944.1|FL383944
EST:     GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG

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: 249

GCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC


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

GCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 93

GCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttct ... gctgttgtagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGCGCTCGAAGGATGCCCGCAATgtgcgcttctgacctctgattagtttacgcccttttggttttgttgttcatgtgcccctgttgttgatgatcacgtgccttgtgctgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG