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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagttcttcataacttcttgcaccggttttaagtgtattgtctattgtctcgttcgttttaatcatttcgcctgttctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG

Basic information

species Zea mays
transcript GRMZM2G151614_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 6
gtacaagt---tcttcataacttcttgcaccggttttaagtgtattgtctattgtctcgttcgttttaatcatttcg--cctgttctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG
||||||||   |||||||||  | ||  || ||||  |||||||||||||        ||||| ||||||||||| |   ||| | |||| ||| || ||||||||||||| || ||||| || || || ||||||||   ||||||||||||||| |||||||||||||| |||||| | ||||||
gtacaagttcctcttcataaactgttaaactggttgcaagtgtattgtctg-------gttcgatttaatcatttggagtctgatatcttttagGCTGAGTGGGGCCCTCTCCGTAGTGTGCGCGTAATTAAGGAACGATCTTCTGGCATGTCTCGGGGATTTGCTTTTATCGACTTCCCTACTGTG

upper sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT3G54230.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacaagttcttcataacttcttgcaccggttttaagtgtattgtctattgtctcgttcgttttaat-catttcgcctgttctcttg-tagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG
    ||  |||||||   || ||| | | || |    |    | |  |   | |     |  | | | ||||   ||  |   | || ||| || | ||||| ||| | |    ||| ||||| ||   ||| |  |||||||| || ||||||||||||||||||||||| ||| |||| |||
--gtaaactcttcat--ttttttgaatctgtatgtcctcaggtttaaacaatttttcatgcatgacttcattattcccatgtgcatgctagGCTGAATGGGGTCCTTTGCATCATGTTCGTGTTATTCGGGAGCAAAATTCTGGGATTTCTCGTGGATTTGCTTTTATTGATTTCCCCACGGTG

upper sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 3'ss of exon 4
gtacaagttcttcataact-tcttgcaccggtt-ttaagtgtattgtctattgtctcgttcgttttaatcatttcgcc----tgttctcttgt-agTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG
|||| | |||| | | | | | || |   |  | | |  || | || |   || ||   | ||||  | ||||    |    | | || || | || || | ||||| || || ||   ||| |||||||| || ||||| | ||||||||| ||||| ||||||||||||||||| ||  |  |||||
gtacta-ttctacttgattcttttactttgaatatcatttggaatgccctctgccttccttgtttataacattctttcaacatttactgttattagGCTGAATGGGGACCCCTTCGGCATGTTCGTGTGATTAAAGAACGAAGTTCTGGCATATCTCGAGGATTTGCTTTTATTGATTTTCCTTCTGTG

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|32837224|gb|CD976902.1|CD976902
EST:     TCAAGGGACTGTCTATGAAGACTAATGATGATGACCTATATCAGATTCTT                         TCTCAGTGGGGCCCTCTACGCAGTGT
genomic: TCAAGGGACTGTCTATGAAGACTAATGATGATGACCTATATCAGATTCTTgtacaagttc ... tctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGT
EST: gi|33467338|gb|CF244387.1|CF244387
EST:     TCAAGGGACTGTCTATGAAGACTAATGATGATGACCTATATCAGATTCTT                         TCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCT
genomic: TCAAGGGACTGTCTATGAAGACTAATGATGATGACCTATATCAGATTCTTgtacaagttc ... tctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCT

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: 46 (upstream exon), 45 (downstream exon)
Score: 34

GCCCCATCTGCCACTGTTGTTGTCAAGGGACTGTCTATGAAGACTAATGATGATGACCTATATCAGATTCTTgtacaagttc ... tctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 23

GCCCCATCTGCCACTGTTGTTGTCAAGGGACTGTCTATGAAGACTAATGATGATGACCTATATCAGATTCTTgtacaagttc ... tctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 28

GCCCCATCTGCCACTGTTGTTGTCAAGGGACTGTCTATGAAGACTAATGATGATGACCTATATCAGATTCTTgtacaagttc ... tctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 54

GCCCCATCTGCCACTGTTGTTGTCAAGGGACTGTCTATGAAGACTAATGATGATGACCTATATCAGATTCTTgtacaagttc ... tctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgtattgtctattgtctcgttcgttttaatcatttcgcctgttctcttgtagTCTCAGTGGGGCCCTCTACGCAGTGTACGTGTGATCAAGGAACGGAATTCTGGCATGTCTCGTGGATTTGCTTTTATTGACTTCTCCACTGTG
                          ttttaat  putative branch site (score: 54)
                                   tttcgcctgttctctt  putative PPT
                          ttttaatcattt  TA-rich tract