Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCCCGCGACGCTAACCGACGCAATGGCGACGCTCACCGTTCCTTCCTCCGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactcacgggcgcgcgctctcgatgcacgcgcaccgacgactgacgcgctctgcgtttcgatcgcag

Basic information

species Zea mays
transcript GRMZM2G061950_T02
intron # 1
splice site 5'
intron type U2

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|37379602|gb|CF626547.1|CF626547
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCCTTCGAAG                         GTTGGGGCACCAACGAGAAACTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|148959272|gb|EC905354.2|EC905354
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|14208237|gb|BG841915.1|BG841915
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|31557932|gb|CD527144.1|CD527144
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|28568972|gb|CB280847.1|CB280847
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|211359810|gb|FL457845.1|FL457845
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|211291869|gb|FL363130.1|FL363130
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGGCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|37378094|gb|CF625705.1|CF625705
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCCTTCGAAG                         GTTGGGGCACCAACGAGAAACTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|14244662|gb|BG842600.2|BG842600
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|149205514|gb|ES701110.1|ES701110
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|37374405|gb|CF623556.1|CF623556
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCCTTCGAAG                         GTTGGGGCACCAACGAGAAACTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|149205542|gb|ES701138.1|ES701138
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|18659292|gb|BM500261.1|BM500261
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|211440499|gb|FL341607.1|FL341607
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAG                         GTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGGCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|37379833|gb|CF626682.1|CF626682
EST:     CGAGGACTGCGAGCAGCTCCACAAGGCCTTCGAAG                         GTTGGGGCACCAACGAGAAACTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|40334431|gb|CK368501.1|CK368501
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCCTTCGAAG                         GTTGGGGCATCAACGAGAAACTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|37376042|gb|CF624517.1|CF624517
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCCTTCGAAG                         GTTGGGGCATCAACGAGAAACTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG
EST: gi|40303683|gb|CK348070.1|CK348070
EST:     CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCCTTCGAAG                         GTTGGGGCACCAACGAGAAACTGATCATCTCCATCCTGGCCCACCGCAACG
genomic: CGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACG

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: 126

CACCCCGCGACGCTAACCGACGCAATGGCGACGCTCACCGTTCCTTCCTCCGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 381

CACCCCGCGACGCTAACCGACGCAATGGCGACGCTCACCGTTCCTTCCTCCGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 233

CACCCCGCGACGCTAACCGACGCAATGGCGACGCTCACCGTTCCTTCCTCCGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 440

CACCCCGCGACGCTAACCGACGCAATGGCGACGCTCACCGTTCCTTCCTCCGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactca ... tcgatcgcagGTTGGGGCACCAACGAGAAGCTGATCATCTCCATCCTGGCCCACCGCAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCCCGCGACGCTAACCGACGCAATGGCGACGCTCACCGTTCCTTCCTCCGTCCCGGCCGTCGCCGAGGACTGCGAGCAGCTCCACAAGGCTTTCGAAGgtcttactcacgggcgcgcgctctcgatgcacgcgcaccgacgactgacgcgctctgcgtttcgatcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC