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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGGCGTGGCAAGGCGGAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctctctctctctctctcacgcgcacgcacagttgtctctgtgtcctgaatgctgcactacttccgttattgcag

Basic information

species Zea mays
transcript GRMZM2G071620_T01
intron # 8
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|78085638|gb|DV514031.1|DV514031
EST:     CCAGAACACTTTTTTGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|78104752|gb|DV523170.1|DV523170
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|116824571|gb|EC868205.1|EC868205
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|211236050|gb|FL156597.1|FL156597
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|30031660|gb|CB833511.1|CB833511
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|18174972|gb|BM350360.1|BM350360
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|71762711|gb|DR960648.1|DR960648
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|50326014|gb|CO521140.1|CO521140
EST:     CCAGAACACTTTTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|32165114|gb|CD670432.1|CD670432
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|71434192|gb|DR815242.1|DR815242
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|71444521|gb|DR825571.1|DR825571
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|31558052|gb|CD527264.1|CD527264
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|211514993|gb|FL455541.1|FL455541
EST:     CCAGAACACTTCTTCGTGSCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|32836421|gb|CD976099.1|CD976099
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGC
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGC
EST: gi|91878815|gb|EB408772.1|EB408772
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
EST: gi|148980768|gb|EE027336.2|EE027336
EST:     CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTAC                         ATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTG

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

AATTGGCGTGGCAAGGCGGAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTGCTACCCTCCTGCGTGGATGGCTTAGCCAGCGCTTTGGTTCCATTGCCTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 23

AATTGGCGTGGCAAGGCGGAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctc ... gttattgcagATACCATACTATGGACATGAACCAGCAGCCAGAGCCAGCGCCGGGCGGCTGCTACCCTCCTGCGTGGATGGCTTAGCCAGCGCTTTGGTTCCATTGCCTT




<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGGCGTGGCAAGGCGGAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCTTCGTGGCTCTGGAGAGCAACGCGCCTCTGCAACCTACgtaattcctctctctctctctctcacgcgcacgcacagttgtctctgtgtcctgaatgctgcactacttccgttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA