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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcccccgtggagcaattttgctctcctccttttcacacccgtctgaaattaacgcaggttagattgactgggattctttcccccttttcttcttgttcgtaaattcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCGCATATGTGTACATCTCCTTCTTCCCGAGTGAGCATGTGGTGGA

Basic information

species Zea mays
transcript GRMZM2G068557_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068557_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g36720.1 (Oryza sativa), 3'ss of exon 1
gtacgcccccgtggagcaattttgctc---tcctccttttcacacccgtctgaaattaacgcaggttagattgactgggattctttcccccttttcttcttgttcgtaaattcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCGCATATGTGTACATCTCCTTCTTCCCGAGTGAGCATGTG---GTGGA
||||       |  || || | | | |   |  ||| |  |    |  ||   ||||   |||    | |   | ||  |     |    ||||| || ||         ||||||||||| ||||||||||  | ||||||||||| ||||||||| | |||  ||| || || || |||||||||  |||||||||||| ||| |    |||||
gtacagaattctcaagaaaatctccccaagttttccatcccctctctttccccaattt-tgcaatcaaaagcaagtgaaagaacctaaagcttttttttttt------ggttcttgcagGGAGTATTTTCCTCGCATTCAGCGCGCCGATTCTGATCGTCGCGGCTCTGGCGTACGTCTACATCTCCGCCTTCCCGAGTGACCATATCCATGTGGA
















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|148995962|gb|EE035209.2|EE035209
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|149097278|gb|EE183101.2|EE183101
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|149113069|gb|EE191505.2|EE191505
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|71320477|gb|DR796977.1|DR796977
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|149080339|gb|EE169357.2|EE169357
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|50329460|gb|CO524586.1|CO524586
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|211358194|gb|FL287114.1|FL287114
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGTCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|149014577|gb|EE044221.2|EE044221
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|211358200|gb|FL287120.1|FL287120
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGTCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|148930967|gb|EC873482.2|EC873482
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|149088601|gb|EE177718.2|EE177718
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|148964973|gb|EC906060.2|EC906060
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|211234051|gb|FL287109.1|FL287109
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGTCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|149086545|gb|EE176089.2|EE176089
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|211234044|gb|FL287102.1|FL287102
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGTCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|149088071|gb|EE177251.2|EE177251
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|211234045|gb|FL287103.1|FL287103
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGTCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|148949541|gb|EC895005.2|EC895005
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|211234047|gb|FL287105.1|FL287105
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGTCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|148955766|gb|EC901465.2|EC901465
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
EST: gi|211234052|gb|FL287110.1|FL287110
EST:     GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGTCG                         GGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG
genomic: GTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCG

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 2 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 9 (downstream exon)
Score: 1

ACCTGGGCCGCGGGGATCTTCCTCTACCCGACCAAGCCCGTGCAGGCCGTGTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCGCATATGTGTACATCTCCTTCTTCCCGAGTGAGCATGTGGTGGA


Block sizes: 41 (upstream exon), 30 (downstream exon)
Score: 4

ACCTGGGCCGCGGGGATCTTCCTCTACCCGACCAAGCCCGTGCAGGCCGTGTTCAGGAAGTGGGTCGGGCTCACCAGGGACTCCATGTTCGGCATCGCCGgtacgccccc ... attcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCGCATATGTGTACATCTCCTTCTTCCCGAGTGAGCATGTGGTGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagattgactgggattctttcccccttttcttcttgttcgtaaattcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCGCATATGTGTACATCTCCTTCTTCCCGAGTGAGCATGTGGTGGA
    gattgac  putative branch site (score: 4)
                ttctttcccccttttc  putative PPT
                                          taaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcccccgtggagcaattttgctctcctccttttcacacccgtctgaaattaacgcaggttagattgactgggattctttcccccttttcttcttgttcgtaaattcttgcagGGGGTATTTTCCTGACCTTCAGCGCGCCAATTCTGATCATTGCGCTTCTCGCATATGTGTACATCTCCTTCTTCCCGAGTGAGCATGTGGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA