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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtcatgagtctccttagcttccgttctactcacttttatgatatttttttctgcagaacttaattaggttaacatggtcttagtgcgtatctc...

Basic information

species Zea mays
transcript GRMZM2G141587_T05
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 5'ss of exon 12
CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtcatgagtctccttagcttccgttctactcacttttatgatatttttttctgcagaacttaattaggttaacatggtcttagtgcgtatctc
 |||||||| || ||||||||||||||| | |||||||||||||| ||||||||||||||||||||| |||| ||||||||||||||||| |||||    | |      || |||    |     | |  |   || ||     | |  | ||  |    ||    |  |  |   | || |  |  ||  |||
TAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAGgtaccatctgccctatcccctataatatttctttgtttttttctacctattctcatgcttaatcttttgcacacctgtattagatcgtgctcagttgctc

upper sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 21
CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgt--cttctgtcatgagtctccttagcttccgttctactcacttttatgatatttttttctgcagaacttaattaggttaacatggtcttagtgcgtatctc
 |||||||| || ||||||||||||||| | |||||||||||||| ||||||||||||||||||||| |||| ||||||||||||||||| |||||  | ||||||     | |||    |        ||| || |||  || | ||  |           ||| | | |||  |||  |   ||   | ||  |
TAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAGgtaccatctgtctcttttttccccctccaaaagg-tacccagtttc-tggtgttaatactgatgatttttagtgatgtttccatcctaacaggcagaatgcc
















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|67013287|gb|CO442036.1|CO442036
EST:     CCAGCAA-GTCCCTGAGATTGTAGCATTGTGGAAAAAG-ATCTCCAGAAG                         GTAA-CTCAAA-GCAGCAGAGTCGCTGGCTGATCCTA-TGAGTACCCAA-C
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|32931477|gb|CF036289.1|CF036289
EST:     CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTA
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTA
EST: gi|211291668|gb|FL235608.1|FL235608
EST:     CAAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCCTA-TGAGTACCCAAA
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCC-TAATGAGTACCCAAA
EST: gi|60337474|gb|DN204447.1|DN204447
EST:     CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCATAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|6095376|gb|AW120043.1|AW120043
EST:     CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCA
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCA

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: 253

CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 395

CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 477

CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtcatgagtctccttagcttccgttctactcacttttatgatatttttttctgcagaacttaattaggttaacatggtcttagtgcgtatctc

- - - - - - - - - - - - - - - - - - - - - - -  GCAAAG