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

...cactcataagtgcaatatagtaatcgcagtatgattgtatgaaacttagaggttgtacaagctgtactgacaataagctgggaataccgtaatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA

Basic information

species Zea mays
transcript GRMZM2G042552_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042552_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 3
----cactcataagtgcaatatagtaatcgcagtatgattgtatgaaacttagaggttgtacaagctgtactgacaataagctgggaataccgtaatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA
     | |      || |   ||  | | | |     |||   |  | |||  ||  ||       |||||| |||||||  ||  |   |  | | ||||||||||| || ||||| || ||||| || |||||||| ||||| |||||||||||||||||   ||| |||||||| || ||||| || ||||| ||||||||
ctcatattacattttgtagagtatcatttgtaagtgtattcctttcatcttccagactgat--gtttgtacttacaataaattgcaac--ctatcacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA

upper sequence: GRMZM2G042552_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S104_29V6.1 (Physcomitrella patens), 3'ss of exon 3
-cactcataagtgcaatat--agtaatcgcagtatgattgt--atgaaacttagaggttgtacaagctgtactgacaataagctgggaataccgtaatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA
 || |  | | ||   | |  |   || |   | ||||  |  ||| |   ||| |  |||| | | | | |||||     | || | || |      ||| |||| || || ||| | ||||| ||  ||   || ||||||||||| ||||||||||| |||  |||||||||||| || || || |||||||| ||||| ||
ccaattgttaatgggttgtcaacagattggcatctgatgttcgatgcaggatagtgactgta-atggttttctgactgattgttgtgtattcga----cttgcagCCACGGCGAGGGCGGTAGGGCAACTGCAGAAAAGCACTGAAGTTATGAAACTTGTAAACAACCTCATGAAAGCTCCTGAAGTGGCAGCCACCATGCAAGA
















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|87154823|gb|DY399612.1|DY399612
EST:     GAACAAGGCCCAGCTCAAATCCATCTCCATGCACCTTGGTGAAATAGTTG                         CTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCATTGAAGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC
EST: gi|44901356|gb|CK827901.1|CK827901
EST:     -ACAAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTG                         CTACTGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC
genomic: AAC-AAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC
EST: gi|32834245|gb|CD973923.1|CD973923
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTG                         CTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC
EST: gi|113702321|gb|EE679825.1|EE679825
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTG                         CTACTGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC
EST: gi|60399737|gb|DN232547.1|DN232547
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTG                         CTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAAC

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: 43 (upstream exon), 48 (downstream exon)
Score: 86

CTGGCCATGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTACGAGAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 74

CTGGCCATGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTACGAGAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 80

CTGGCCATGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTACGAGAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 61

CTGGCCATGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTACGAGAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCGTTGgtactaataa ... aatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaggttgtacaagctgtactgacaataagctgggaataccgtaatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA
                   tactgac  putative branch site (score: 61)
                                               tctttc  putative PPT
                                            taatcttt  TA-rich tract