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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacagtctctgtgcatttttgccgtgcattccaagcaatatacacatcccttgaagtctgtaacccatccctttttttctgaacgaatcggaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGGCGAGGCCAGGTCGTGAAGATCATCAGGCCCAGCGAGACGGCGGGCAGAT

Basic information

species Zea mays
transcript GRMZM2G476009_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G476009_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g59140.1 (Oryza sativa), 3'ss of exon 3
-----gacagt-ctctgtgcatttttgccgtgcattccaagcaatatacacatcccttgaagtctgtaacccatccctttttttctgaacgaatcggaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGGCGAGGCCAGGTCGTGAAGATCATCAGGCCCAGCGAGACGGCGGGCAGAT
      |  || | || ||||||| | | ||   || | |||||||  | ||    |   ||| ||||||  ||   || ||||||||| |    ||  |||| |||||||||||||||| || ||||| |||||||| |||||||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || |||||||
gcatgcatggtgcgctctgcatttgt-cagtatgttgctagcaata--cgcagtattaatagtatgtaactaat---ttcttttctgaatgtgatgggacaaatagCTTCCAAGAATACAAATTACGGACCCTATTGCAAGGTACTATGGCCTCAGACGAGGACAGGTTGTGAAGATCATCAGGCCCAGCGAGACAGCCGGCAGAT
















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|149013010|gb|EE042745.2|EE042745
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|5499455|gb|AI855322.1|AI855322
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|78124667|gb|DV543051.1|DV543051
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|16925901|gb|BM078969.1|BM078969
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|37388912|gb|CF631671.1|CF631671
EST:     ATGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTCAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|14243487|gb|BG841206.2|BG841206
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|120480234|gb|EH210778.1|EH210778
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|71762794|gb|DR960731.1|DR960731
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTCAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|149001167|gb|EE038432.2|EE038432
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|5871454|gb|AW017925.1|AW017925
EST:     ATGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTCAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|211038261|gb|FL216363.1|FL216363
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGGAACTCAG                         CTTCCAAGAATACAGATCACGGATCCAATTGCTAGATACTACCGCCTCAAG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
EST: gi|149001168|gb|EE038433.2|EE038433
EST:     ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAG                         CTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG
genomic: ACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGG

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: 36

TATAAACATCAAGGAACATGTCCTTGTTCCTGAGCATCAGGTGCTCACAAACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGGCGAGGCCAGGTCGTGAAGATCATCAGGCCCAGCGAGACGGCGGGCAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 735

TATAAACATCAAGGAACATGTCCTTGTTCCTGAGCATCAGGTGCTCACAAACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGGCGAGGCCAGGTCGTGAAGATCATCAGGCCCAGCGAGACGGCGGGCAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 830

TATAAACATCAAGGAACATGTCCTTGTTCCTGAGCATCAGGTGCTCACAAACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGGCGAGGCCAGGTCGTGAAGATCATCAGGCCCAGCGAGACGGCGGGCAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

TATAAACATCAAGGAACATGTCCTTGTTCCTGAGCATCAGGTGCTCACAAACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgtattggcgc ... gaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGGCGAGGCCAGGTCGTGAAGATCATCAGGCCCAGCGAGACGGCGGGCAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcccttgaagtctgtaacccatccctttttttctgaacgaatcggaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGGCGAGGCCAGGTCGTGAAGATCATCAGGCCCAGCGAGACGGCGGGCAGAT
            ctgtaac  putative branch site (score: 210)
                          tttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacagtctctgtgcatttttgccgtgcattccaagcaatatacacatcccttgaagtctgtaacccatccctttttttctgaacgaatcggaccaaacagCTTCCAAGAATACAGATCACGGATCCTATTGCTAGGTACTACGGCCTGAGGCGAGGCCAGGTCGTGAAGATCATCAGGCCCAGCGAGACGGCGGGCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - gtgcatt
- - - - - - - - - - - - tgcattc
- - - - - - - - - - - - - - - -caagcaa
- - - - - - - - - - - - - - - - - - - - - cacatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacgaa