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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggccacccattctctgcccgactgcccctctgtctctctctctctctagcacagcacacttcgaatttaaaatgccatttccttttttctggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT

Basic information

species Zea mays
transcript GRMZM2G341404_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g74580.2 (Oryza sativa), 3'ss of exon 1
ggccacccattctctgcccgactgcccctctgtctctctctctctctagcacagcacacttcgaatttaaaatgccatttccttttttctggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT---------------------------------------------
                                          | ||    |   | |       | | |  ||    |||||  |  | |    |||||||||| ||||| || || ||  |||||||||||  || ||||||||  |||||| |||| ||||| ||||||||  | ||||| |||||||||||||||||                                             
-----------------------------------------gtttcctttatgcctcctggtagactaagtatcatttttcccctcattt----tttcagaaggccaagataatgatccctctactttgttcaaacgagcctcagAAATGATGAACCTAAGGAAATATGATGGATCACTTGGTCTGCTAAATGCTGTGTTGGAGGTTGACCCAAATCACTCAGAAGCTTACAGGCAGCGTGCATC

upper sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g74580.1 (Oryza sativa), 3'ss of exon 1
ggccacccattctctgcccgactgcccctctgtctctc-----tctctctctagcacagcacacttcgaatttaaaatgccatttccttttttctggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT
         || ||   || | |  | ||  ||||        |   | | |     |   | | | | |    || |  |||||      |  |    |||||||||| ||||| || || ||  |||||||||||  || ||||||||  |||||| |||| ||||| ||||||||  | ||||| |||||||||||||||||
---agtttcttttcactccaattagcactacgtctacacaaaatggatgtttcctttatgcctcctggtagactaagtatcatttttcccctcattt--tttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGATGAACCTAAGGAAATATGATGGATCACTTGGTCTGCTAAATGCTGTGTT

upper sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10180.1 (Oryza sativa), 3'ss of exon 2
---ggccacccattc---tctgcccgactgcccctctgtctctctctctctctagcacagcacacttcgaatttaaaatgccatttccttttttctggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT
     |    |||||   || || | ||  |  | |    |   | | ||  |    |  |    |    | | |  || |  |||||  |  | |    |||||||||| ||||| || || ||  |||||||||||  || ||||| ||  |||||| |||| ||||| ||||||||  | ||||| ||||||||||||||| |
agtttcttttcattccaatcagcactacgtctacacaaaatggatgtttcctttatgcttcctggt--agactaagtatcctttttcccctcattt----tttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGATGAACCTAAGGAAATATGATGGATCACTTGGTCTGCTAAATGCTGTGCT

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|148940996|gb|EC885847.2|EC885847
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|149079408|gb|EE168385.2|EE168385
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|211247225|gb|FL156665.1|FL156665
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|148970832|gb|EE021601.2|EE021601
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|78080724|gb|DV509136.1|DV509136
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTCTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|71323581|gb|DR798459.1|DR798459
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|211247229|gb|FL156669.1|FL156669
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|87155508|gb|DY400297.1|DY400297
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|78104565|gb|DV522983.1|DV522983
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|211247228|gb|FL156668.1|FL156668
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|91875154|gb|EB405111.1|EB405111
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|211247230|gb|FL156670.1|FL156670
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|149010182|gb|EE041997.2|EE041997
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|148960799|gb|EE011462.2|EE011462
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|211245008|gb|FL156664.1|FL156664
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|149081738|gb|EE170891.2|EE170891
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|211247231|gb|FL156671.1|FL156671
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|211247226|gb|FL156666.1|FL156666
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|26558848|gb|CA831083.1|CA831083
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|101391578|gb|EB817725.1|EB817725
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|22546040|gb|BU098361.1|BU098361
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|88758107|gb|DY542248.1|DY542248
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
EST: gi|148940390|gb|EC885183.2|EC885183
EST:     CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAG                         AAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA
genomic: CATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGA

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: 210

GAGATCATGGTGCGGGCATGGGGGCGGCGGACGGCGCTGCCTCCGCTCCTCATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GAGATCATGGTGCGGGCATGGGGGCGGCGGACGGCGCTGCCTCCGCTCCTCATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

GAGATCATGGTGCGGGCATGGGGGCGGCGGACGGCGCTGCCTCCGCTCCTCATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 477

GAGATCATGGTGCGGGCATGGGGGCGGCGGACGGCGCTGCCTCCGCTCCTCATCCTTGGCCTCCTCCGCCTGCACTACTCCTCGCTGGTCGTCGCCCAAGgtgcacctcc ... ggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcacagcacacttcgaatttaaaatgccatttccttttttctggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT
                             ccatttccttttttct  CT-rich tract
              ttcgaatttaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggccacccattctctgcccgactgcccctctgtctctctctctctctagcacagcacacttcgaatttaaaatgccatttccttttttctggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - -cattctc
- - - - - - - - - - -ctgcccc
- - - - - - - - - - - - - - - - - - - - - - - - - acagcac