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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA

Basic information

species Zea mays
transcript GRMZM2G135904_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
              ||     ||| || || ||     || ||   |||||           |  |    |||     |    ||  |  |  || | || || |   ||   |||  ||  ||   || | |           ||||||||||  ||||||||||||| ||||| |||||||||||||||||||||||||| ||||| ||||||||| ||||||||||||| || ||||||||||| |||||||||||
-------------gtaagcttaactac-tgataatc-cccaattccccaaga----------acctacttgaccaccattaaacacatagttctgttgattta-tcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA

upper sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP02733 (Chlamydomonas reinhardtii), 3'ss of exon 4
gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
                                                         |  |   | ||  | | ||  |||    |   |    | | | |  ||   |  |  |      |  |        |||||  |    ||       |||||| || || ||||| || || || ||||||||||| || ||||| ||||| ||||||||||| || |||||||                            
---------------------------------------------------------tgcagggtggtggggcggtgctggcg-gtgcaccggcgctgaccctgtccctcctcctccccgctcgt-----cccgctccgggtc-cctccccccctgcagccaagGTGTTCCACCGCGACCTCAAGCCCAAGAACATCCTGGCCAACTCCGACTGCAAACTCAAGATATGTG----------------------------

upper sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
                                                 |    ||   |||||||     |   | |||| | ||   || |||  | |   || | | |||  ||| |       | | ||||| ||    |    |  || |  |||||||||||| ||||| ||||| ||||| |||||| || |||| ||| | || ||||| |||||||| ||||| ||||||||||| || |   | |||| 
-----------------------------------------------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgt---gtgtctcgtttggatgt-------tgacgtgcttctatttgg--gtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG

upper sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
                                               ||   |  |   | ||      |||||| || | |        |  ||| | ||| || |||| || ||       ||| | | ||  || |    || |    | || |||||||||| || ||||| || || ||||| |||||  |  |||| ||| | ||||| ||||||||||| ||||||||||||||||| || |   | || | 
----------------------------------------------tcacaactctcactgtac--aaaagactgatgggatgtggtcctttttggatttct-gtctgtttttgtgg------atgttgacgtcttcat----gtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAG

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|67016391|gb|CO445140.1|CO445140
EST:     CCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCG                         CTAATGTATTCCATCGCGATCTAAAGCCCAAGAATATACTGGCTAACTCGG
genomic: CCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCGgtaagtatat ... attggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGG
EST: gi|22545672|gb|BU098031.1|BU098031
EST:     CCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCG                         CTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGG
genomic: CCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCGgtaagtatat ... attggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
     tgttatgatatattat  TA-rich tract