Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctgtgttagagtggctggaaaccctaaccctaaacaggctgggctgttgtatatatattagagacataaatacatgggttggaccaaagccca...

Basic information

species Zea mays
transcript GRMZM2G129987_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129987_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 5'ss of exon 5
AGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctgtgttagagtggctggaaaccctaaccctaaacaggctgggctgttgtatatatattagagacataaatacatgggttggaccaaagccca---------
||||||| |||||||||||||||||||| |||||||||||||||||||| |||| |||||||||||| || || ||||||| ||| |||||||||||||||||  ||      |  ||||      ||   |  |  || | | |        ||| |  |  || |  |   |  ||   |   ||        ||||          
AGGCTGATATTGAAGAATTTGAAGCTAAGTACAGAGGGTCAGATTCTGAAAAAAAGGACTTGAAGGATCTATATACAAAATTTAAAGGCAACATGAACAGgtggcttacaaaatttagtgttgattaatttt--ctatacagaaggcaatgaattgcaagtgaataattgggttccatttctattttaatttggtgcccttgtatgcag
















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|78111290|gb|DV529687.1|DV529687
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|211238012|gb|FL479475.1|FL479475
EST:     CTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: CTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|31664549|gb|CD573482.1|CD573482
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|19436724|gb|BM953134.1|BM953134
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|149009177|gb|EE041301.2|EE041301
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|91053239|gb|EB163657.1|EB163657
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|76011893|gb|DT939063.1|DT939063
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|71771230|gb|DR969167.1|DR969167
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|78082398|gb|DV510810.1|DV510810
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|19057616|gb|BM736283.1|BM736283
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|19436292|gb|BM952702.1|BM952702
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|71320398|gb|DR796949.1|DR796949
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|71771229|gb|DR969166.1|DR969166
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|78026730|gb|DV495117.1|DV495117
EST:     GGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: GGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|67022325|gb|CO451074.1|CO451074
EST:     ATAAGGGTAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: ATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|19436725|gb|BM953135.1|BM953135
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTGGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|91054843|gb|EB165261.1|EB165261
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|76924244|gb|DV169873.1|DV169873
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|33098018|gb|CF057978.1|CF057978
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
EST: gi|60341606|gb|DN208579.1|DN208579
EST:     ACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT
genomic: ACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 175

AGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 26

AGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 49

AGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG


Block sizes: 36 (upstream exon), 44 (downstream exon)
Score: 25

AGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctg ... atctatccagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctgtgttagagtggctggaaaccctaaccctaaacaggctgggctgttgtatatatattagagacataaatacatgggttggaccaaagccca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA