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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgctcttgaatccattctgctggtttttgatgtctaagaagataaacccccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC

Basic information

species Zea mays
transcript GRMZM2G149751_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 9
-------------------gtcagtgctcttgaatccattctgctggttttt---gatgtctaagaagataaaccc-ccataccatgagtgtagtc-----------gcatttaattgactttattggcctatgttcta------cagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC
                   ||  ||| | |  |  |  | |  |||| | ||   ||   | ||  | ||| |        | ||| |    |||            ||||| || | |  | |||||| | | || ||      |||||||||||||||||||||||||||||||||||||| || |||||||| ||||||||||| || |||||||| |||||||| ||| |||| |||||||| |
gtcagtatccttgtgtactgtttgtgttttctagactttgcacctggctgtttgagaaaacaaaataaatatatttattgaagcattaacaaagtttggtttgttctgcattgaagtaagctaattggcatgtattttatactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGGTGTGTCAAGCCAC

upper sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 10
--------------------------gtcagtgctcttgaatccattctgc---tggtt-tttgatg------tctaagaagataaacc--cccataccatgagtgtagtc------gcatttaattgactttattggcctatgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC
                           | |||| |  | | |  | | | |   ||| | |||||        | | |  ||||  |    | |||      ||| | ||       ||||| || | |  | | |||| | | || |||||||||||||||||||||||||||| ||||||||||| || |||||||| || ||||||||||| |||||||| || ||||| ||  |||| |||||||| |
gtcagtatcctcgtgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaacaatattattagatttattgactcattaacaaagtttggtttgttctgcattgaagtaagctaactggcatgtattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTTACTGCCAATGGATGGGTGCAATCCTATGGATCCCGGTGTGTCAAGCCAC

upper sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
gtcagtgctcttgaatccattctgctggtttttgatgtctaagaagataaacccccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC
                                           | |||    |   || |||| | ||       || ||||  ||   |||| ||| | |||  ||||||||||| ||||||||||||||||||||||||||    |||||||| ||||| | ||| || ||||| ||||| || || ||  |||| || ||||| |
-----------------------------------------gtaggatttggcag-attccataactg-------atctaatctac---attgtcct-ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC

upper sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ05611 (Selaginella moellendorffii), 3'ss of exon 8
gtcagtgctcttgaatccattctgctggtttttgatgtctaagaagataaacccccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC
                                               ||         |   |     |||  | || ||||  ||   |||| ||| | |||  ||||||||||| ||||||||||||||||||||||||||    |||||||| ||||| | ||| || ||||| ||||| || || ||  |||| || ||||| |
----------------------------------------------gtaggatttggcagatt--ccatagctg-atctaatctac---attgtcct-ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC

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|33100706|gb|CF060666.1|CF060666
EST:     AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|18963575|gb|BM660512.1|BM660512
EST:     AGCTCCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|149087939|gb|EE177184.2|EE177184
EST:     AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|22473206|gb|BU037686.1|BU037686
EST:     AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|21432208|gb|BQ547698.1|BQ547698
EST:     TGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCTGTT
genomic: TGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGC-GTT
EST: gi|33100968|gb|CF060928.1|CF060928
EST:     AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
EST: gi|32802578|gb|CD954814.1|CD954814
EST:     AGCTTCAAGAAGAGCTTGTCATTGATGTGCTTGTGCATGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC
genomic: AGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctc ... tgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC
                          aattgac  putative branch site (score: 3)
                      atttaattgactttat  TA-rich tract