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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttcttgcctgccttttcttaaaagcttttggcttttgtaaagttgcacttgatcaaatgtgcttttactatgatgtatgggtgacaggatatgt...

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 10
TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttcttgcctgccttttcttaaaagcttttggcttttgtaaagttgcacttgatcaaatgtgcttttactatgatgtatgggtgacaggatatgt---
||||| ||||||||||| ||||||||||||||||||||||||||||| || || || |||||||||||||||||| | ||| ||    |  |     |    |||   |    ||  || |  | |     ||  ||  |   ||| ||||    || |    | | |   
TTCCATATTCTTTTCTGTGTATTTTCTGCTGTGGCTCCTCCTGTTGTCTTCGAGGGGAAATCATTGGCgtaagttccctgcttgttcatattct---gtcaatgggaatatggaaactgaaactaaaagggtgacctacttgcatgttgtacaaatggctttttttatcag

upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G11180.2 (Arabidopsis thaliana), 5'ss of exon 9
TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttcttgcctgccttttcttaaaagcttttggcttttgtaaagttgcacttgatcaaatgtgcttttactatgatgtatgggtgacaggatatgt
 ||||||| ||||||||| | ||| |||| || ||||||||| |||| ||  ||||||||||| | ||||||||||| |  |   ||||     |  |  |  ||    |||||    |    || |||| |||    | |   |||  |||                
CTCCACATACTTTTCTGCCTCTTTGCTGCAGTTGCTCCTCCTATTGTCTTCAAAGGAAAATCACTTGCgtaagtttcctcacaagctttaagacatcgtctaggg----tgtaacacagttaatgttcaagtgtctgatgatcttgaaatatacag------------
















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|60342784|gb|DN209757.1|DN209757
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|32906331|gb|CF011144.1|CF011144
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGAT
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGGAT
EST: gi|149103005|gb|EE288366.2|EE288366
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|76018526|gb|DT945696.1|DT945696
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|29543932|gb|CB604312.1|CB604312
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|78023022|gb|DV491409.1|DV491409
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     TATTTTCTGCTGTGGCTCCTCCCTGT-GTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: TATTTTCTGCTGTGGCTCCTCC-TGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|110944605|gb|EE164762.1|EE164762
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|166654883|gb|EG281590.1|EG281590
EST:     TTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
genomic: TTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC                         AGGAATTTTGCCAGC
genomic: GTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGC

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), 47 (downstream exon)
Score: 77

TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 128

TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 91

TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 199

TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttct ... acttttgcagAGGAATTTTGCCAGCAATTGATCTTATTAGCGTGAATGCTTTGGTTGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGCgtaagtttcttgcctgccttttcttaaaagcttttggcttttgtaaagttgcacttgatcaaatgtgcttttactatgatgtatgggtgacaggatatgt

- - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA