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'   
13  
 5'  3'   
14  
 5'  3'   
15  
 5'  3'   
16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccacattcttatacagatgacaaacagttactgatcattatgaatgactaccaaattttcttaatacaacacatcatcgcattctagttatgct...

Basic information

species Zea mays
transcript GRMZM2G416120_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 3
TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccacattcttatacagatgacaaacagttactgatcattatgaatgactac-caaattttcttaatacaacacatcatcgcattctagttatgct
|||||||||||| ||||||||||| ||||||||||||||| ||||| ||||||||||||||||||||||||| || |||||||||||||||||||||||||||||| ||| | || | || || | || | | || ||| ||| |||| | || | | || ||| | ||
TGCTGCCAAGGATATCAAGTTTGGAGTTGAGGCCCGTGCTTTGATGCTGAGGGGTGTTGAGGAGTTGGCAGATGCAGTCAAAGTGACAATGGGTCCTAAGgtataattgtgttcatgtaaatgtgtcattgtgcacttgtgtact-tgtctgaatacgttaattgttttgtagctattataaatgaagttcctttgataga

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 3
TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgta--taaccacattctt-ata--cagatgacaaaca--gttactg-atcattatgaa------tgactaccaaattttcttaa--tacaacacatcatcgcattctagttatgct-----------------------------------------------------------------------
||| ||||| ||||| ||||||||||| ||||| || ||||||||| | | |||||| || ||| | || || || || ||||| |||||||| ||||||||| || | || | | ||| || |||| || ||| | |||| | | || |||||| | || | || || | ||||| || |
TGCGGCCAAAGACATTAAGTTTGGTGTGGAGGCTCGGGCTCTGATGCTTAAGGGTGTCGAAGAGCTCGCTGATGCCGTTAAAGTAACAATGGGCCCTAAGgtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtgttgatcacgattgttttgttaaacttgtgtttttttag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 3
TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgta--taaccacattcttatacagatgacaaacagttactgatcattatgaatgactaccaaatttt-cttaatacaacacatcatcgcattctagttatgct
||| || || ||||| || |||||||| ||||| || ||||||||| | | ||||||||| ||| | || || ||||||||||| || |||||||| |||||| | | ||| |||| | || | || | || | || | |||| || | | | | | | | |
TGCGGCTAAAGACATTAAATTTGGTGTGGAGGCTCGGGCTCTGATGCTTAAGGGTGTTGAAGAGCTTGCTGATGCTGTCAAAGTAACCATGGGTCCCAAGgtaactgaatggattgttatttgctttttggtttatt--tagatggggaagattattattattttatacttattagcaacggtaaggggaaagtgttggaac-

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 3
TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccacattcttatacagatgacaaacagttactgatc--attatgaatg--actaccaaattttcttaatacaacacatcatc-gcattctagttatgct-----
||||||||| ||||| ||||||||||| |||||||| ||| ||||| | | ||||||||| ||| | || || || |||||||| || ||||| ||||||||| |||| | |||| | | |||| || || ||||| || | | | || | || | | || | | || | | | |
TGCTGCCAAAGACATTAAGTTTGGTGTGGAGGCCCGGGCTTTGATGCTTAAGGGTGTTGAAGAGCTCGCCGATGCCGTCAAAGTAACCATGGGCCCTAAGgta--accaagct--------gatgcctgatagtttcttttcttgttatgtctgctagtgaaagatatctttggcaaagtgtggcacctgtgtttttatcaatcatttat

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|91054374|gb|EB164792.1|EB164792
EST:     GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
EST: gi|71758555|gb|DR956492.1|DR956492
EST:     GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
EST: gi|149073906|gb|EE162234.2|EE162234
EST:     GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
EST: gi|78078492|gb|DV506905.1|DV506905
EST:     GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
EST: gi|211348396|gb|FL389757.1|FL389757
EST:     GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
EST: gi|149077207|gb|EE165873.2|EE165873
EST:     GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
EST: gi|19770413|gb|BQ035134.1|BQ035134
EST:     GGGGTGTTGAGGAGTTGGCAGACGCGGTCAAAGTGACAATGGGTCCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
EST: gi|71425565|gb|DR806757.1|DR806757
EST:     GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAG

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), 48 (downstream exon)
Score: 502

TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 246

TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 374

TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccac ... ccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGCCAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGACGCTGTCAAAGTGACAATGGGTCCTAAGgtataaccacattcttatacagatgacaaacagttactgatcattatgaatgactaccaaattttcttaatacaacacatcatcgcattctagttatgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaaaca