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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttagttattgcttgattctgcatatcaattattagctaatttggtagctgcagcttcactattattgctccaaaaggccagtgttgaccatcttcctttctttttgtaacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

Basic information

species Zea mays
transcript GRMZM2G366935_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 5
gtgtgttagttattgcttgattctgcatatcaattattagctaatttggtagctgcagcttca--ctattattgctccaaaaggccagtgttgaccatctt--cctttctttttgt---aacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG
    ||  || |||| ||||||||||||||||||| ||| | |||| ||||||||| | ||||  ||  | |||||  ||| |  ||   |||||||||||  ||||||||| |     || |||||||||||| ||  | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||  |||||| || | |||
----gtgtgtgattgtttgattctgcatatcaattcttaacaaattcggtagctgctgattcattcttctgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG

upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtgtgttagttattgctt-----gattctgcatatcaattatt--agctaatttggtagctgcag-------cttcactattattgctccaaaaggccagtgttgacc--atcttcctttctttttg-----taacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG
                                         || | ||| ||  |          |||   || |||  || ||   ||   ||| ||   | |||       | ||  ||||||   |           || || ||   || |||||| ||||         ||||||| ||||||| ||  |  | ||||| ||||| |||||||||||||| ||||| ||||| || ||||||| ||||||  |||| ||  | |||
gtgtgtgcattgtccttggcccttgctttatctctcattctgtattttattttctaacctaaccaattacccagatctgttttttgggcctgttttgtttgtccaggactgtacctctgtattatgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG
















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|21331443|gb|BQ486824.1|BQ486824
EST:     TGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCAT                         ATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATAC
genomic: TGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgttagt ... tttgtaacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATAC
EST: gi|148930529|gb|EE285130.2|EE285130
EST:     TGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCAT                         ATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATAC
genomic: TGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgttagt ... tttgtaacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATAC

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), 47 (downstream exon)
Score: 140

GGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgttagt ... tttgtaacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 109

GGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgttagt ... tttgtaacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 152

GGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgttagt ... tttgtaacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG


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

GGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgttagt ... tttgtaacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattattgctccaaaaggccagtgttgaccatcttcctttctttttgtaacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG
                        tgttgac  putative branch site (score: 80)
                          ttgaccatcttccttt  CT-rich tract
                                       tttcttttt  TA-rich tract