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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTCGACTCAGAAAGGTGGGGCATACGCTGCCAAGCTGCTTTCAGTAAGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttctactcctgtcttgtttccatgttgcttcaccaacgaatgcacagttcacataacccttattatcatcactgcttcccatgaataactagct...

Basic information

species Zea mays
transcript GRMZM2G157068_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157068_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g03410.1 (Oryza sativa), 5'ss of exon 11
GGAGCTCGACTCAGAAAGGTGGGGCATACGCTGCCAAGCTGCTTTCAGTAAGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttctactcctgtcttgtttccatgttgcttcac-caacgaatgcacagttcacataacccttattatcatcactgcttcccatgaataactagct
 ||||| ||||| |||||||||||| |||||||||| ||||||||||| || |||||||| || ||||| ||||| ||||| || || |||||||||||||||| |||| | ||||||  ||| | ||||||| || |   | | |   || | ||     |     |  | |  ||          || | |   ||   
TGAGCTTGACTCTGAAAGGTGGGGCCTACGCTGCCAGGCTGCTTTCAGCAAATTTGATCTGGATGGTGACGGATACATCACTCCAGATGAACTCAGAATGgtaagtttcaattcctgttctgtgttcatgttggtttatgtagctacctcatatttagtgaatgaagtgattttgtccacagaagatattatttcttaca-
















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|78113086|gb|DV531480.1|DV531480
EST:     AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATG                         ---CA-CAC--TGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
genomic: AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
EST: gi|71765451|gb|DR963388.1|DR963388
EST:     AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATG                         ---CA-CAC--TGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
genomic: AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
EST: gi|113704348|gb|EE681852.1|EE681852
EST:     AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAA--                         -T---GCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
genomic: AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
EST: gi|78113085|gb|DV531479.1|DV531479
EST:     AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAA--                         -T---GCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
genomic: AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
EST: gi|149082401|gb|EE171588.2|EE171588
EST:     AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAA--                         -T---GCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
genomic: AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
EST: gi|71330882|gb|DR802236.1|DR802236
EST:     AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATG                         GTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC
genomic: AGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCC

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: 49 (upstream exon), 47 (downstream exon)
Score: 13

GGAGCTCGACTCAGAAAGGTGGGGCATACGCTGCCAAGCTGCTTTCAGTAAGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCCGACATCGACAAAGACGGCAAGATAAGCCTGTCCGAGTTCCGCAAGCTCC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 41

GGAGCTCGACTCAGAAAGGTGGGGCATACGCTGCCAAGCTGCTTTCAGTAAGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCCGACATCGACAAAGACGGCAAGATAAGCCTGTCCGAGTTCCGCAAGCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GGAGCTCGACTCAGAAAGGTGGGGCATACGCTGCCAAGCTGCTTTCAGTAAGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCCGACATCGACAAAGACGGCAAGATAAGCCTGTCCGAGTTCCGCAAGCTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 24

GGAGCTCGACTCAGAAAGGTGGGGCATACGCTGCCAAGCTGCTTTCAGTAAGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttct ... ttctttcaagGTGCAGCACACTGGGTTGAAGGGATCTATCGAGCCGCTGCTGGAGGAGGCCGACATCGACAAAGACGGCAAGATAAGCCTGTCCGAGTTCCGCAAGCTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCTCGACTCAGAAAGGTGGGGCATACGCTGCCAAGCTGCTTTCAGTAAGTTTGATCTTGACGGTGATGGATATATCACGCCGGAGGAACTCAGAATGgtaattttctactcctgtcttgtttccatgttgcttcaccaacgaatgcacagttcacataacccttattatcatcactgcttcccatgaataactagct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA