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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgtaactataggtcacacgatgattattttctccgcgacattatccgggtattaccgtgacagatatttttattggctccatttctgccatgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAAATCGCCTGCTGCTGCGCTGGTCAACAACTCCCTGACCAGATTCGGGCAG

Basic information

species Zea mays
transcript GRMZM2G006468_T03
intron # 1
splice site 3'
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|60399773|gb|DN232583.1|DN232583
EST:     CAGACCATTGGGACTCCCTCGTGCGTTTTCC-AATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|211186705|gb|FL252850.1|FL252850
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATAGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|37420659|gb|CF648025.1|CF648025
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|211522061|gb|FL312388.1|FL312388
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|14242681|gb|BG840373.2|BG840373
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|211436012|gb|FL361903.1|FL361903
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|211186703|gb|FL252848.1|FL252848
EST:     AGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGTCAG                      
genomic: AGACCATTGGGACTCCCTCGTGCGTTTTCC-AA--A-TCAGgttcgttctt ... atgtagt
EST: gi|211316809|gb|FL363634.1|FL363634
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|211453015|gb|FL324462.1|FL324462
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|211186707|gb|FL252852.1|FL252852
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGTCAG                      
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCC-AA--A-TCAGgttcgttctt ... atgtagt
EST: gi|76010926|gb|DT938096.1|DT938096
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGTCAG                      
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCC-AA--A-TCAGgttcgttctt ... atgtagt
EST: gi|89755427|gb|DY685847.1|DY685847
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAAGGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|13178341|gb|BG349599.1|BG349599
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|211134484|gb|FL356345.1|FL356345
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|74242180|gb|DT650094.1|DT650094
EST:     TGGGACTCCCTCGTGCGTTTTCCAAATCAG                         GTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
genomic: TGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAA
EST: gi|32918930|gb|CF023742.1|CF023742
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGTCAG                      
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCC-AA--A-TCAGgttcgttctt ... atgtagt
EST: gi|211186704|gb|FL252849.1|FL252849
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         T
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcag-
EST: gi|211186704|gb|FL252849.1|FL252849
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         T
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcag-
EST: gi|211186704|gb|FL252849.1|FL252849
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         T
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcag-
EST: gi|211186704|gb|FL252849.1|FL252849
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAG                         T
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcag-
EST: gi|71774337|gb|DR972215.1|DR972215
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGTCAG                      
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCC-AA--A-TCAGgttcgttctt ... atgtagt
EST: gi|78113266|gb|DV531659.1|DV531659
EST:     CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGTCAG                      
genomic: CTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCC-AA--A-TCAGgttcgttctt ... atgtagt

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), 41 (downstream exon)
Score: 27

CAAGTTGCCTCGTGCTCTGCTTCTTCGGTTTTCAGGAGCGTCGGCCATTGCTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAAATCGCCTGCTGCTGCGCTGGTCAACAACTCCCTGACCAGATTCGGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CAAGTTGCCTCGTGCTCTGCTTCTTCGGTTTTCAGGAGCGTCGGCCATTGCTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAAATCGCCTGCTGCTGCGCTGGTCAACAACTCCCTGACCAGATTCGGGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 225

CAAGTTGCCTCGTGCTCTGCTTCTTCGGTTTTCAGGAGCGTCGGCCATTGCTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAAATCGCCTGCTGCTGCGCTGGTCAACAACTCCCTGACCAGATTCGGGCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 51

CAAGTTGCCTCGTGCTCTGCTTCTTCGGTTTTCAGGAGCGTCGGCCATTGCTGCTGGAAAAGCAGACCATTGGGACTCCCTCGTGCGTTTTCCAAATCAGgttcgttctt ... atgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAAATCGCCTGCTGCTGCGCTGGTCAACAACTCCCTGACCAGATTCGGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgggtattaccgtgacagatatttttattggctccatttctgccatgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAAATCGCCTGCTGCTGCGCTGGTCAACAACTCCCTGACCAGATTCGGGCAG
               acagatatttttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgtaactataggtcacacgatgattattttctccgcgacattatccgggtattaccgtgacagatatttttattggctccatttctgccatgtagtcagGTTGATGGCGATGGAGGGACCAGTTTTATGCCGCCCTGCAATGCAAGCCAAATCGCCTGCTGCTGCGCTGGTCAACAACTCCCTGACCAGATTCGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC