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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttttttattgtgtttggtgttggatattttttgtttgcttcttttctttatttctgacttgccatcagttatatataagtggctttacttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTCAACATTTGAAAATGATCTTCTTCTAGAG

Basic information

species Zea mays
transcript GRMZM2G000749_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 6
--------------tcttttttattgtgtttggtgttggatattttttgtttgcttcttttctttatttctgact-tgccatc-agttatatataagtg-gctttacttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTCAACATTTGAAAATGATCTTCTTCTAGAG
                   | | ||   |||  | | |  || | ||   | | || | | ||  || | | ||| |  |||| |||| ||   |  ||    | ||| |||  |||||||||||||||||||||||||||||||||||| || ||||| || |||||   |||||| || | |||||| |||| ||| ||||||||||||||||||
gtgtttaacctatagaccctatctttcatttattttggtttagtcttgcctcgtttttgtcctacatgttttactatttcatccagttttacccacttgcaaataactcctgtacagGTATGCTAGAGAAGATACACACTATCTGTTGTATATGTATGACTTGATGAGGTTGAGACTGCAAAAGGAGTCGACATCTGACAATGATCTTCTTCTAGAG

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 7
tcttttttattgtgtttggtgttggatattttttgtttgcttcttttctttatttctgacttgccatcagttatatataagtggctttacttctgcc--cagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTC-AACATTTGAAAATGATCTTCTTCTAGAG
 ||| |||||  || ||   | | |||  ||  ||      | |  |    | | || | | |  || | |   || ||| |  || |  || ||    ||| ||||| |||||||||||||||||||||||||| ||||| || ||||||||    |   ||        ||| ||    |   || | |||   |||  | 
-cttgtttatcttggttttagcttgatgattactggcacactgtcatgggcaat-ctaattagtaattattacaatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA-

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 6
-tcttttttattgtgtttggtgttggat-attttttgtttgcttcttttcttt-atttctgacttgccatcagttatatataagtggctttacttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAG-ACAGAG--ACTACAGAGGGAGTCAACATTTGAAAATGATCTTCTTCTAGAG
   || ||  ||| | ||| | || | |   |  ||    |  |  | || |  |   |  | || |  | |  |||   | | |   | |  ||     ||| ||||| |||||||||||||| |||||| | |||||||||||||| ||||| |  |||  | |    | |           ||||| || |     || |   
aatttattccttgagcttgctattagcttgatagttaccagtatactgtcatggacaccctaattactgtaatctat---tgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA---

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 6
tcttttttattgtgtttggtgttgg-atattttttgtttgcttcttttctttatttctgacttgccatcagttatatataagtggc---tttacttctgcc--cagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTCAACATTTGA-AAATGATCTTCTTCTAGAG
                    ||| | ||||| | ||| |  |   | || | |||     |||  |||  |||   |  |  |  |   ||| | | |     ||| |||||||||||||||||||| ||||| |||||||| |||||| ||||| ||  |    | || |    | |||     ||  |   ||||   |||    
--------------------gttagtatattctctgtctagtctctctcatgatt----gctttgcattggttgagttgagctaacacatttgcatataatggcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT-

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 6
tcttttttattgtgtttggtgttggatattttttgtttgct-tcttttctttatt--tctgacttgccatcagttatatataagtggctttacttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTCAACATTTGAAAATGAT-CTTCTTCTAGAG
                      |  || || | |||    | |||||||  || |  |||| | |    | | ||      |  |   |  | |||    ||| ||||| ||||||||||| ||||| || || ||||||||||||||||| | ||    ||| |||||   | |||    |||     || ||   |||    
---------------------gtcaatcttctctgtcctttgtcttttcactactgttctggcctaagttgacttgagctcacatttttggatttccctgcagATATGCAAGAGAAGATACCCACTACCTCTTATACATATATGATTTAATCAAACTAGAACTGCAGAGAATGGCAAAGGATGACGCGCATACTGACTCTCCT-

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0056g01320.t01 (Vitis vinifera), 3'ss of exon 5
tcttttttattgtgtttggtgttggatattttttgtttgcttcttttctttatttctgacttgccatca-gttatatataagtggctttacttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTCAACATTTGAAAAT---GATCTTCTTCTAGAG
  ||| ||  |   |    | || | | | |  ||  |  |   ||  |  |  |    | |   |||   | | ||     |   |||  |  || | || |||||||| ||||||||||||||| |  || | ||||||||||||||||||     | | |       | |     | || |||    ||  |||| ||   
gttttctttcttcatgaattctttgttgtctcatgactattatgttgttgcaccttgatcctctgatctcatcaaattcttttattttttatgatgac-agATATGCTAGGGAAGATACACACTATTTACTGCATATATATGATTTAATGAGAACCCAATTGCTCTCAATGGCTGAGCTGGAGAATTCTAATGCTCTTTTA---

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|211021453|gb|FL457596.1|FL457596
EST:     TATCAAAATGCAGACTGGAGGTCGAGACCMCTTCCTGATGAAATGATCAA                         GTATGCTAGAGAAGATACMCMCTATCTGTTGTACATATATGATTTAATGAG
genomic: TATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAAgtattgtgca ... ttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAG
EST: gi|60341236|gb|DN208209.1|DN208209
EST:     TATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAA                         GTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAG
genomic: TATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAAgtattgtgca ... ttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAG
EST: gi|60338799|gb|DN205772.1|DN205772
EST:     TATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAA                         GTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAG
genomic: TATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAAgtattgtgca ... ttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttatttctgacttgccatcagttatatataagtggctttacttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTCAACATTTGAAAATGATCTTCTTCTAGAG
        ttctgac  putative branch site (score: 2)
                                       ctttacttctgccc  putative PPT
                    atcagttatatataa  TA-rich tract