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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttaatggatcctgcattcacaccaagtttgtcaaagtaaatacttttcgctcatccttttatctcgtaaaatctaccttacctgtgctgtttttagGCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCTTCGTCAATCCCTTGCAAAAAATGATAGACGA

Basic information

species Zea mays
transcript GRMZM2G377311_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 2
atatttaatggatcctgcattcacaccaagtttgtcaaagtaaatacttttcgctcatccttttatctcgtaaaatctaccttacctgtgctgtttt-tagGCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCTTCGTCAATCCCTTGCAAAAAATGATAGACGA
   |    || || || |||       |  |||    |  ||   | | |    |||| || |   ||   ||    |  ||  | | || | | |  |||||| ||||| || ||||| ||||| || || |||||||| ||||||||||||||||| |||| |||||||||||||||||||
-ggtcatgtgaatactacatattgtttagtttttcttatttatggagtataatatcattctgtctacttccaatcaatgactgccttttgttctgtggtagGCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA

upper sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
--------atatttaatggatcctgcattcacaccaagtttgtcaaagtaaatacttttcgctcatccttttatctcgtaaaatctaccttacctgtgctgtttttagGCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCTTCGTCAATCCCTTGCAAAAAATGATAGACGA
         | ||| ||   |  |  ||   |  |||   ||    || ||||| |||    |  |  ||  |   | | |     |   |     |  |  ||  |||||||| || || ||||| ||||||||  |||| ||||| ||||| | |||||||||||||| |||||| ||||| ||| | 
atttcctactgttttattatttttttat--gcctcaaacatg----agcaaatagtttataattgtttttccag--catcactgtgattatgaacattttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG

upper sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 3
atatttaatggatcctgcattcacaccaagtttgtcaaagtaaatacttttcgctcatccttttatctcgtaaaatctaccttacct-gtgctgtttttagGCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCTTCGTCAATCCCTTGCAAAAAATGATAGACGA
 |   |     |||     || |   |   |    |  | |   |   ||||  | |  |||     | ||  | | ||     |||  ||        || ||||||||||| ||||| || || || |||||||| ||||| |||| || ||| ||||| | |||||||||||| ||||  
ctcggtgtataatcacctgttaagctccgttcctgctcactgcttgactttca-ttaggcttgatcttagtgtattttattaatcctcatggaaaccgcagTCCCCAAGTGACTATTGCAACTGCCATTGTATTCTGCCATCGGTTTTTCCATCGACAATCACATGCAAAAAATGACAGACTT

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|211518784|gb|FL067253.1|FL067253
EST:     CGGAAGTTATATTGCAAGTTTCTACAAGAGTTGGGCATGGCGCTTAAAAT                         GCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCT
genomic: CGGAAGTTATATTGCAAGTTTCTACAAGAGTTGGGCATGGCGCTTAAAATgtaagattgg ... ctgtttttagGCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCT
EST: gi|211518785|gb|FL067254.1|FL067254
EST:     CGGAAGTTATATTGCAAGTTTCTACAAGAGTTGGGCATGGCGCTTAAAAT                         GCCCCAAGTGACG
genomic: CGGAAGTTATATTGCAAGTTTCTACAAGAGTTGGGCATGGCGCTTAAAATgtaagattgg ... ctgtttttagGCCCCAAGTGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttcgctcatccttttatctcgtaaaatctaccttacctgtgctgtttttagGCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCTTCGTCAATCCCTTGCAAAAAATGATAGACGA
                                 accttac  putative branch site (score: 3)
                                             ctgttttt  putative PPT
                         taaaatcta  TA-rich tract