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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAACAATCATCTCTCCTGTCAAAACTTACTCGTCAACTCAGTATCCATGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgctattttcgttatctgtttattgactaagattcctggccaaacaaacatattagctggcgattattacttgataaagcagttctattagtcc...

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 21
------CAAAAACAATCATCTCTCCTGTCAAAACTTACTCGTCAACTCAGTATCCATGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagct-gctat--tttcgttatctgtttattgactaagattcctggccaaacaaacatattagctggcg-attattacttgataaagcagttctattagtcc
      |||||||||||||||||| ||||||| ||||| |||||||| ||| ||||||| ||||||||      | | |||||| | ||||| | | ||||||| ||||||||  ||||  ||||  |  |||   | | |     | | |      |    |  |   | ||      | | || ||| ||| |  |||| ||||    
AAATACCAAAAACAATCATCTCTCTTGTCAAAGCTTACCCGTCAACTTAGTGTCCATGACAACAGGGC------TGCTTCTTATGCCAATGATATCTCTGAAGCTGgtaagcttactatactttcaatgcctgagaagtaatagcaaatacaattgtatggtattttacatctcctttgtaactagttgttaatgttgttc-attac---
















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|4314677|gb|AI438584.2|AI438584
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|31362644|gb|CD447001.1|CD447001
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|211132356|gb|FK982423.1|FK982423
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|78543683|gb|DV621181.1|DV621181
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|211033868|gb|FL466120.1|FL466120
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACMCCACTGAAGCCG                         AGAGCCCTCGAACACCAAGCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|19769804|gb|BQ034525.1|BQ034525
EST:     CAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: CAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|24768960|gb|CA404089.1|CA404089
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|37400988|gb|CF637855.1|CF637855
EST:     ATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAAGCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: ATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|71773970|gb|DR971858.1|DR971858
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|149108496|gb|EE189682.2|EE189682
EST:     TGATAACAGGGCATCTGTTTCCTTTTATTTTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|14243758|gb|BG841389.2|BG841389
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|211006912|gb|FL435020.1|FL435020
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|26455909|gb|CA827492.1|CA827492
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|31355296|gb|CD439653.1|CD439653
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|6989671|gb|AW447884.1|AW447884
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGGGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|56382295|gb|CV984964.1|CV984964
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAAGTCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|31357385|gb|CD441742.1|CD441742
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|149096022|gb|EE181696.2|EE181696
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|67026008|gb|CO454757.1|CO454757
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAAGCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|87151847|gb|DY396636.1|DY396636
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGGACACCAAGCCGC
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGC
EST: gi|24769886|gb|CA405015.1|CA405015
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|16926444|gb|BM079512.1|BM079512
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|19769907|gb|BQ034628.1|BQ034628
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACTCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|5296189|gb|AI782869.1|AI782869
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|211132361|gb|FK982428.1|FK982428
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCGAACACCAAGCCGCTCAAGTGAGGACTGGAGGTCAGCTTTTG
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTG
EST: gi|109637318|gb|EC590863.1|EC590863
EST:     TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCG                         AGAGCCCTCAAACACCAAGTCGCTCAGGTGGGGACTGGGAGGTCAGCTTTT
genomic: TGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGG-AGGTCAGCTTTT

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: 211

CAAAAACAATCATCTCTCCTGTCAAAACTTACTCGTCAACTCAGTATCCATGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTGATTCCGCTTCAAATGGTCCTGTTGCTGGAAGCACAAACAGTCAATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 246

CAAAAACAATCATCTCTCCTGTCAAAACTTACTCGTCAACTCAGTATCCATGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTGATTCCGCTTCAAATGGTCCTGTTGCTGGAAGCACAAACAGTCAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 383

CAAAAACAATCATCTCTCCTGTCAAAACTTACTCGTCAACTCAGTATCCATGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTGATTCCGCTTCAAATGGTCCTGTTGCTGGAAGCACAAACAGTCAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

CAAAAACAATCATCTCTCCTGTCAAAACTTACTCGTCAACTCAGTATCCATGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgct ... ttatttgcagAGAGCCCTCGAACACCAACCCGCTCAGGTGAGGACTGGAGGTCAGCTTTTGATTCCGCTTCAAATGGTCCTGTTGCTGGAAGCACAAACAGTCAATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAAACAATCATCTCTCCTGTCAAAACTTACTCGTCAACTCAGTATCCATGATAACAGGGCATCTGTTTCCTCTTATTCTAATGACACCACTGAAGCCGgtaagctgctattttcgttatctgtttattgactaagattcctggccaaacaaacatattagctggcgattattacttgataaagcagttctattagtcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacaaa