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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctacatagaagcgatgaaacaaagataaacaagagtggtaattagaaagttcagtttgttcaggtaactcaacacaagaaaatattattttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCATGAAATTGAAAAGTGTTCCGGCAGAGGAATTATTGTTACAGGGCCAGCGC

Basic information

species Zea mays
transcript GRMZM2G050325_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050325_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g16146.1 (Oryza sativa), 3'ss of exon 3
tctacatagaagcgatgaaacaaagataaacaagagtggtaattagaaagttcagtttgttca--ggtaactcaacacaagaaaatatta-ttttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCATGAAATTGAAAAGTGTTCCGGCAGAGGAATTATTGTTACAGGGCCAGCGC
  || |  | |    |   |  || | ||| |||| |||  |  |   ||||    |||||||   ||   | |  || | |  ||  |    | ||||||||||||| ||||| || ||||| |||||||||||||| || ||||||||| |||||||| |||| |||   || |||||| |||||||||| || ||||| |
-ttataatggattttttttattaaaa-aaagaaga-tggagaggaaggagttggaattgttcatttgtttgttagtactaaatgattctggcatggctttcagGTGGAACTTTCTTCCGGAAAAGAGGTTGCTGATATTATCCCTAACATTAATGAAATTAAAAAATGTGATGGTAGAGGAGTTATTGTTACGGGACCAGCAC
















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|18171147|gb|BM340987.1|BM340987
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|71317982|gb|DR795750.1|DR795750
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|50338931|gb|CO534057.1|CO534057
EST:     TTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: TTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|74239407|gb|DT647321.1|DT647321
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|94477663|gb|EB706621.1|EB706621
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|71775486|gb|DR973364.1|DR973364
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|60356851|gb|DN223824.1|DN223824
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|50331530|gb|CO526656.1|CO526656
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|148986829|gb|EE030628.2|EE030628
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|37375249|gb|CF624050.1|CF624050
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|37376720|gb|CF624915.1|CF624915
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|149097405|gb|EE183258.2|EE183258
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|50331531|gb|CO526657.1|CO526657
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|93015163|gb|EB640683.1|EB640683
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|33099705|gb|CF059665.1|CF059665
EST:     GTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|44901068|gb|CK827613.1|CK827613
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
EST: gi|78119655|gb|DV538039.1|DV538039
EST:     GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATT                         GTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT
genomic: GAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCAT

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: 48 (upstream exon), 44 (downstream exon)
Score: 74

TGTTGATTGCCATCCTTCCGAGCTGCCGGCAATCCCCGACACCCTCAACGGAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCATGAAATTGAAAAGTGTTCCGGCAGAGGAATTATTGTTACAGGGCCAGCGC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 190

TGTTGATTGCCATCCTTCCGAGCTGCCGGCAATCCCCGACACCCTCAACGGAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCATGAAATTGAAAAGTGTTCCGGCAGAGGAATTATTGTTACAGGGCCAGCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 412

TGTTGATTGCCATCCTTCCGAGCTGCCGGCAATCCCCGACACCCTCAACGGAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCATGAAATTGAAAAGTGTTCCGGCAGAGGAATTATTGTTACAGGGCCAGCGC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 39

TGTTGATTGCCATCCTTCCGAGCTGCCGGCAATCCCCGACACCCTCAACGGAGCCTCCATTGTCAGCGTTCACAAGTCAACGACGGCCGGTGACCTCATTgtaattctcc ... ttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCATGAAATTGAAAAGTGTTCCGGCAGAGGAATTATTGTTACAGGGCCAGCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaagttcagtttgttcaggtaactcaacacaagaaaatattattttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCATGAAATTGAAAAGTGTTCCGGCAGAGGAATTATTGTTACAGGGCCAGCGC
                 aggtaac  putative branch site (score: 39)
                                           ttttgctttc  putative PPT
                          aacacaagaaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctacatagaagcgatgaaacaaagataaacaagagtggtaattagaaagttcagtttgttcaggtaactcaacacaagaaaatattattttgctttcagGTGGAGCTTTCATCAGGAAAGGAGGTTGCTGATATCATTCCTAACATTCATGAAATTGAAAAGTGTTCCGGCAGAGGAATTATTGTTACAGGGCCAGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA