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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgttcgtaattcacaataaatgaatatcttcttattgattttagctggcatgtagattgttggtgcagtgagtgaagtgtgctctcacagtgtt...

Basic information

species Zea mays
transcript GRMZM2G157310_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157310_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g44660.1 (Oryza sativa), 5'ss of exon 3
AGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgt-actacgttcgtaattcacaataaatgaatatcttcttattgattttagctggcatgtagattgttggtgcagtgagtgaagtgtgctctcacagtgtt
|||||||||||||||| || | | |||   ||||||||||||||||||||||||||||||||||||| ||| | |||||||||||||||||||||||||||| |  | ||   | | | |  |    || | || | |    |  | |    ||| |    |||     |     ||          | ||||| |||   
AGTACGACGCCAAGAGGGAGGAGCTGTTCGAGCACTACCACCCCATCGAGATCTGCCCCGACATCCCGCTCCCCGAGAAGGCCAAGCTCATGGAAGAATGgtgaggaagtagtttagtgagtagtgctgcaaatttccaccctattatcctttggtacaccgatcaggtggattctgttgtggtcaagttctca-agtccc
















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|28566667|gb|CB278315.1|CB278315
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|101386461|gb|EB815247.1|EB815247
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|5268576|gb|AI770540.1|AI770540
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|76293679|gb|DV033247.1|DV033247
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|101385767|gb|EB814932.1|EB814932
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|9951997|gb|BE638580.1|BE638580
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTC
EST: gi|74242168|gb|DT650082.1|DT650082
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|78092209|gb|DV520583.1|DV520583
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|211095811|gb|FL316687.1|FL316687
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGACAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|211143628|gb|FL314871.1|FL314871
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGACAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|91048046|gb|EB158464.1|EB158464
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|91877197|gb|EB407154.1|EB407154
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|91050984|gb|EB161402.1|EB161402
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|211118716|gb|FL311656.1|FL311656
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|31354764|gb|CD439121.1|CD439121
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|71438827|gb|DR819877.1|DR819877
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|50333544|gb|CO528670.1|CO528670
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
EST: gi|71449422|gb|DR830472.1|DR830472
EST:     ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATG                         GTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC
genomic: ATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGC

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: 109

AGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGCTATCACAAAATCTGTCTCTGATGCCGCAATTGCTTTCAGAGAGGGTGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 39

AGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGCTATCACAAAATCTGTCTCTGATGCCGCAATTGCTTTCAGAGAGGGTGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 63

AGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGCTATCACAAAATCTGTCTCTGATGCCGCAATTGCTTTCAGAGAGGGTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

AGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgtt ... tgtgctacagGTGGGAGAAGACTCATGGTCTTCTTATTGAAGGCGGTCTTACATACGAAGCTATCACAAAATCTGTCTCTGATGCCGCAATTGCTTTCAGAGAGGGTGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCCACTCTCGGAGAAGGCCAAGCTCATGGAAGAATGgtactacgttcgtaattcacaataaatgaatatcttcttattgattttagctggcatgtagattgttggtgcagtgagtgaagtgtgctctcacagtgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaataaa