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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcag

Basic information

species Zea mays
transcript GRMZM2G127948_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127948_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g06980.3 (Oryza sativa), 5'ss of exon 2
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcg--aagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcag
|||  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||| |||| || |||||||||||| |           ||||   ||||   ||   | |    |   |  |||  |   || |   |  ||  | |||| ||| |||   | | |                                        
GCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACGgtcagcaacacgcaaatcccccatctct--tccatcgcagatctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcag---------------------------------------

upper sequence: GRMZM2G127948_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcag
||| ||||||||| |   ||||||||| || ||||||||||| || ||||| |||||||| || |||||||| || || || ||||| || |||||||  ||   ||  | |   |  |||  |||    | |           |    |||   |        |    || |||   | || | |                                              
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatctcttcatcctcctct---gttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcatcag--------------------------------------------

upper sequence: GRMZM2G127948_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 5'ss of exon 3
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcag
|||  |||||||||||   |||||||| ||||||||||| ||||||||||| |||||||| || || ||||| || || || ||||| || ||||| | |||| |    || ||             |||||   |||   |     |  |   || |  |   |    |  |    |||| |||  ||    ||||   |   |                           
GCTTCTCAAGCTCATCAATGCCAAGAACACCATGGAGATAGGCGTCTACACTGGCTACTCTCTTCTGGCCACAGCCCTTGCTCTCCCCGATGACGGAAAGgtcgggaaatggtcat-----------agatc-aacacagtaatcatccaagcacgtataa---aaaaatgttatggctgaaaaa--aattggttcttgattgttgcag-----------------------

upper sequence: GRMZM2G127948_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv07s0031g00350.t01 (Vitis vinifera), 5'ss of exon 3
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcag
|||  |||| ||||||  ||||||||| |||||||| |||||||| |||||||||||||||||||||||||| || ||||| || || || ||||| | |||  |      |   | ||| |    ||             ||       |||   || ||    |   |  |  ||  || ||||||||||  |           | ||     ||               
GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacccat----caag-----------acaaaatcaaagaaaaaacactctgtt-tggtttcataga-aaaccaaggaaatgcagagaaaaattttgaccatt---------------

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|50324343|gb|CO519469.1|CO519469
EST:     CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTA
genomic: CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTA
EST: gi|29544906|gb|CB605514.1|CB605514
EST:     CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGC
genomic: CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGC
EST: gi|9952456|gb|BE639039.1|BE639039
EST:     CCGGCTACTCCCTNCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACG                         ATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGC
genomic: CCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGC

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: 44 (upstream exon), 48 (downstream exon)
Score: 96

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 394

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 342

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 617

GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgtt ... cgccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcag

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