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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtcgatattaatagttgcatatgaaaaatgtatctttgagttcttaattgattcaagtctacatttatgttattctttatataatatttgtgg...

Basic information

species Zea mays
transcript GRMZM2G073054_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 5'ss of exon 15
GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtcgatattaatagttgcatatgaaaaatgtatctttgagttcttaattgattcaagtctacatttatgttattctttatataatatttgtgg
|||| |||||  | |||||  | |||||| |||| |||||||| |||||||| || ||||| || ||||| ||  |||| ||||||||||| ||||| ||||| ||  ||   |    | |     |  |  | ||   |   | ||   ||   | ||   |  ||  | | || |      || ||    || | | |
GCGGGATGCCAGCTTTTTGCGTTCCTGTCGAAGACGGTGGTGTGGGTTTTGACTACCGTCTACACATGGCAGTGGCAGATAAATGGATTGAGCTTCTTAAgtatgttctcaggacgtcttggcttttcagtgagattattaagtaagacgttg--ttatatgatactgaactgatatggcgtgttgta----atctctag

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 5'ss of exon 15
GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtcgatattaatagttgcatatgaaaaatgtatctttgagttcttaattgattcaagtctacatttatgttattctttatataatatttgtgg--
| || ||||| ||||| ||||| ||||||||||||||||| ||||| ||||| || ||| | || |||||  |  | || || ||||| ||| | || |||| |||| |     |    | || | | | |      | |  || | |  ||  | ||   |||| |       |  | | ||  || | ||  | |||   
GTGGTATGCCAACATTCTGTATTCCTGTCCAAGATGGTGGCGTTGGATTTGACTACCGTTTACACATGGCCATAGCTGATAAGTGGATAGAAATGCTCAAgtgagtgttt----tctgcattttcttttaagttccatctgctttaatatttggt-gaaataagtgtct-----tactctcctccatgttatgct-gtgaag

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 15
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 5'ss of exon 15
GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtcgata-ttaatagttgcatatgaaaaatgtatctttgagttcttaattgattcaagtctacatttatgttattctttatataatatttgtgg-
||||||||||  |||| ||||| ||||| |||||||||||||| || |||||||||||  | ||||||||  |  | || ||||||||||| ||||| ||||| |     || |  | || ||    | |          ||||    || ||| ||  |  |     | ||| |  | |   |    |   |     ||  
GCGGAATGCCAGCATTCTGTATTCCTGTTCAAGATGGTGGTGTGGGATTTGATTATCGCTTACATATGGCCATTGCTGATAAATGGATTGAGCTTCTTAAgtaggcctctgaaaactcattgtcttctttcttcttcccctcttcatctttttattt--tctagcctcaaattaaattcaggttgagcagtgtgaagatgaa

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|67035192|gb|CO463725.1|CO463725
EST:     GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAA                         GCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
genomic: GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
EST: gi|101386689|gb|EB815361.1|EB815361
EST:     GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAA                         GCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
genomic: GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
EST: gi|211410788|gb|FL280482.1|FL280482
EST:     GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAA                         GCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
genomic: GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
EST: gi|27753880|gb|BM378072.1|BM378072
EST:     GATTATCGTCTTCATATGGCTGTACCAGACAAATGGATTGAACTTCTGAA                         GCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
genomic: GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
EST: gi|32864974|gb|CF004656.1|CF004656
EST:     GAACTTCTGAA                         GCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
genomic: GAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
EST: gi|211410789|gb|FL280483.1|FL280483
EST:     GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAA                         GCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA
genomic: GATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAA

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: 760

GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 221

GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 34

GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtc ... attaccacagGCAAAGTGACGAATATTGGGAAATGGGTGACATCGTGCACACCTTAACAAATAGAAGGTGGCTTGAAAAGTGTGTCACTTATTGTGAAAGTCATGATCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGAATGCCTACATTTTGTATCCCTGTCCAAGATGGTGGTGTTGGTTTTGATTATCGTCTTCATATGGCTGTCCCAGACAAATGGATTGAACTTCTGAAgtaagtggtcgatattaatagttgcatatgaaaaatgtatctttgagttcttaattgattcaagtctacatttatgttattctttatataatatttgtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaaa