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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttggtggcttctgtttgaacatcagtggaactttatatttgctagtggccataagcacatgacttttccttttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG

Basic information

species Zea mays
transcript GRMZM5G807639_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 6
-------------gtgttggtggcttctgtttgaacatcagtggaactttatatttgctagtggccat---aagcacatgact-tttccttttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
              |     |   |||||| |||| |    || || ||   | |      | | | |   ||    || | |   |   | | |||||||| ||||||||||| || ||||| |||||||||||||||||||||
gtacagtcattcaatcactttctgttctgtctgaatagacatgcaatttagcactcatggatagtcttttaaaatgtatcattgcctttctgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
















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|211347968|gb|FL368837.1|FL368837
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTAT
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTAT
EST: gi|211511665|gb|FL408091.1|FL408091
EST:     AGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGANTA-G                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: AGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGA-TAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211042919|gb|FL416910.1|FL416910
EST:     GAGACAGAGTCGAGGCCGATGAAACCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211011070|gb|FL374939.1|FL374939
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTT
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTT
EST: gi|211150258|gb|FL395029.1|FL395029
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211479894|gb|FL423794.1|FL423794
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|67025111|gb|CO453860.1|CO453860
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211137577|gb|FL389523.1|FL389523
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211461966|gb|FL427684.1|FL427684
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCNNTG-TGT-ATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGC--TGGTGTTATTGAAAAG
EST: gi|32862756|gb|CF002438.1|CF002438
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|30306817|gb|CD001490.1|CD001490
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211518170|gb|FL380292.1|FL380292
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211490936|gb|FL402016.1|FL402016
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|31349005|gb|CD433362.1|CD433362
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211157939|gb|FL380349.1|FL380349
EST:     AGACAGAGTCGANGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGCTC
genomic: AGACAGAGTCGA-GGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGCTC
EST: gi|28187901|gb|CB179511.1|CB179511
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211437186|gb|FL418966.1|FL418966
EST:     GAGACAGAGTCGRGGCCGATGAACCCATAGCGCAGATTGAWACTGATAAG                         GTCACTATAGATGTCGCAAGTTCCTGAAGCTGGTGTTATTGAATAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGT-CCTGAAGCTGGTGTTATTGAA-AAG
EST: gi|37420219|gb|CF647798.1|CF647798
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|93017175|gb|EB642695.1|EB642695
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211305586|gb|FL419218.1|FL419218
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211142865|gb|FL377125.1|FL377125
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         -TCCACTATAGATGTCGCAAGTCCTGGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTC-ACTATAGATGTCGCAAGTCCTG-AAGCTGGTGTTATTGAAAAG
EST: gi|211530093|gb|FL390761.1|FL390761
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211235901|gb|FL373720.1|FL373720
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAANGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAA-GTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211431976|gb|FL418926.1|FL418926
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGCTCATT
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGCTCATT
EST: gi|211063833|gb|FL423073.1|FL423073
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211441962|gb|FL416333.1|FL416333
EST:     AGACAGAGTCGANGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: AGACAGAGTCGA-GGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|32834807|gb|CD974485.1|CD974485
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211094733|gb|FL379398.1|FL379398
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAANGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAA-GTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|67031724|gb|CO460473.1|CO460473
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
EST: gi|211539307|gb|FL400264.1|FL400264
EST:     GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG

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), 45 (downstream exon)
Score: 186

AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 345

AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 292

AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 358

AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtgttggtgg ... tttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaactttatatttgctagtggccataagcacatgacttttccttttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG
                                     cttttccttttgttcc  CT-rich tract
      tttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttggtggcttctgtttgaacatcagtggaactttatatttgctagtggccataagcacatgacttttccttttgttccagGTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG