Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcactattctccacagtggggtttcaatgatccatattttgtctagttttttctttttccatgtactgaagggccttagtcattccctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG

Basic information

species Zea mays
transcript GRMZM2G023652_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023652_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g36340.1 (Oryza sativa), 3'ss of exon 6
gtttgcactattctccacagtggggtttcaatgatccatattttgtctagttttttctttttcc---atgtactgaagggccttagtcattccctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG
   |  | ||| | ||| |  ||  || |  | |||||||| ||   |    || |||||| ||    | | ||||   |  |||||  |  | |||   ||||| | |||||| ||||||||||| ||||| ||||||||||| ||| |||||||| ||||||  |||||||| 
--gtatattatac-ccataaaggcattgcgctaatccatatgttcatttacattctcttttccccccttatgctgaccaggtttagtgctgtcttactttcagTTCTACCAAAAACTTGAAGAGAAGATCCATGCAAAGGAGCTTGAACAAACAAATTTGCAGGCAAAATCTAAA
















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|32838814|gb|CD978495.1|CD978495
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTTCTGAGAAGAGAAAGGAG                         TTCTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
EST: gi|21843366|gb|BQ703947.1|BQ703947
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG                         TTCTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
EST: gi|32833164|gb|CD972842.1|CD972842
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG                         TTCTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
EST: gi|21809702|gb|BQ668020.1|BQ668020
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG                         TTCTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
EST: gi|32839274|gb|CD978955.1|CD978955
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTTCTGAGAAGAGAAAGGAG                         TTCTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
EST: gi|31355396|gb|CD439753.1|CD439753
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTTTTGAGAAGAGAAAGGAG                         TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
EST: gi|32837723|gb|CD977401.1|CD977401
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTTCTGAGAAGAGAAAGGAG                         TTCTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
EST: gi|22542624|gb|BU093062.1|BU093062
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG                         TTCTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
EST: gi|31355088|gb|CD439445.1|CD439445
EST:     CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG                         TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA
genomic: CTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACA

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), 49 (downstream exon)
Score: 552

AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 380

AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 436

AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 450

AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAGgtttgcacta ... ctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagttttttctttttccatgtactgaagggccttagtcattccctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG
                                      tcattccct  CT-rich tract
     ttttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcactattctccacagtggggtttcaatgatccatattttgtctagttttttctttttccatgtactgaagggccttagtcattccctacacccagTTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA