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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccctttctctctttctctctctctctctttcccagatctgccacccacccagaccaaggatctttacccctctctgtctctctctctgttgctcgtccccccgcag

Basic information

species Zea mays
transcript GRMZM2G099363_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099363_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g06980.3 (Oryza sativa), 5'ss of exon 2
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccctttctctctttctctctctctctctttcccagatctgccaccca---cccagaccaaggatctttacccctct-ctgtctctctctctgttgctcgtccccccgcag
|||  | ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||  |||| || |||||||||||| |   |    | |   | | |  ||||| ||  || |||||||| ||   |   ||||  | |  ||  |  | |||||| ||  ||    |                      
GCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACGgtcagcaaca---cgcaaatcccccatctct-tccatcgcagatctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcag--------------------

upper sequence: GRMZM2G099363_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccctttctctctttctctctctctctctttcccagatctgccacccacccagaccaaggatctttacccctctctgtctctctctctgttgctcgtccccccgcag
||| ||||||||| |   ||||||||| || ||||||||||| || ||||| |||||||| || ||||||||||| || || ||||| || |||||||  ||   |   |  |||||   ||   |||| | | ||     | | || |   |      |   |   | || | || | |     ||                          
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaat---caatctcttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagt-ttcatcctttttatcatcag------------------------

upper sequence: GRMZM2G099363_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 5'ss of exon 3
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccctttctctctttctctctctctctcttt---cccagatctgccacccacccagaccaaggatctttacccctctctgtctctctctctgttgctcgtccccccgcag
|||  |||||||||||   |||||||| ||||||||||| ||||||||||| |||||||| || || ||||| || || || ||||| || ||||| | ||||||       ||     |   | |  |     |     | |  ||     |        |   ||  |  ||    | |   |||  |                          
GCTTCTCAAGCTCATCAATGCCAAGAACACCATGGAGATAGGCGTCTACACTGGCTACTCTCTTCTGGCCACAGCCCTTGCTCTCCCCGATGACGGAAAGgtcgggaaatggtcatagatcaacacagtaatcatccaagcacgtataaaaaaatgttatggctgaaaaaaattggttcttgattgttgcag------------------------

upper sequence: GRMZM2G099363_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv07s0031g00350.t01 (Vitis vinifera), 5'ss of exon 3
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccctttctctctttctctctctctctctttcccagatctgccacccacccagaccaaggatctttacccctctctgtctctctctctgttgctcgtccccccgcag
|||  |||| ||||||  ||||||||| |||||||| |||||||| |||||||||||||| |||||||||||||| ||||| || || || ||||| | |||  |      |  || |     |       |    ||  |||     ||| |     |       |      |       ||          | |||  | |          
GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacc----catcaagacaaaatcaaagaaaaaacactctgtttggtttcatagaaaaccaaggaaatgcagagaaaaattttgaccatt---------

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|18963317|gb|BM660366.1|BM660366
EST:     GCTACTACAGCTCCTCAGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: GCTACT-C-GCTCCTC-GCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|5510830|gb|AI857214.1|AI857214
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|74238429|gb|DT646343.1|DT646343
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|149014739|gb|EE044420.2|EE044420
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|86474833|gb|DY241203.1|DY241203
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|16916553|gb|BM072891.1|BM072891
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|37379818|gb|CF626673.1|CF626673
EST:     CCGGATACTCGTTCCTGGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|91879069|gb|EB409026.1|EB409026
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|50337681|gb|CO532807.1|CO532807
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|18963587|gb|BM660518.1|BM660518
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|14244780|gb|BG842718.2|BG842718
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
EST: gi|211091281|gb|FL220529.1|FL220529
EST:     CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC
genomic: CCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGC

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: 47 (upstream exon), 49 (downstream exon)
Score: 122

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGCATCAACAAGGCCGGCGTGGGCCACAAGATCGACTTCCGCGAGGGCCCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 242

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGCATCAACAAGGCCGGCGTGGGCCACAAGATCGACTTCCGCGAGGGCCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 612

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGCATCAACAAGGCCGGCGTGGGCCACAAGATCGACTTCCGCGAGGGCCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1551

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccc ... ccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGCATCAACAAGGCCGGCGTGGGCCACAAGATCGACTTCCGCGAGGGCCCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccctttctctctttctctctctctctctttcccagatctgccacccacccagaccaaggatctttacccctctctgtctctctctctgttgctcgtccccccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA