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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC

Basic information

species Zea mays
transcript GRMZM2G179308_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
||||| ||||||||| ||  ||  | ||||    |   |||     | | | |  ||      ||  | || | ||   | |   | | |    |||  | || |||||  |    || | ||||||||||||||||| || |||||||| || ||||||| ||||| | |||||||||| |||||||| ||||||||||||||||| ||||| || ||||| || |
gtatactttgttcttctacctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 6
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttag---tgaatattgaata--tggtactgatcctc--tttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
                                   | | | |     ||  |||  ||   ||| || |  || ||||| ||      | ||   ||   ||  |   ||      || |||  ||||   ||  | || || |||| ||||      | |||| || |||| | ||||||||||| |||||||| || || ||||||||||| |||||||| ||||| | |       
--------------------------------aggaaagtaagaacaccaagtggctga-aattgctatgctattaggtcagatacagaaatgagatcactgacatccattgctgattgtttatatttaacagAGTACAACCAGATCACCAA------GTTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttagt----gaatattgaata-tggtactgat--cctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
                                  || | | |     ||  |||  ||   ||| || |  || ||||| ||     |||   |||  | ||  |   ||  | | || |||  ||||   ||  | || || |||| ||||      | |||| || |||| | ||||||||||| |||||||| || || ||||||||||| |||||||| ||||| | |       
--------------------------------ggaaaagtaagaacaccaagtggctga-aattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgct-tgttgatttctgttgtaataggttagtgaa-tattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
                                      | || || |       || |||       |  |||       || | || |  ||||   || | |  |  |  | ||| |   |||  ||     |||||||  | || ||| | || ||||   ||  | ||||| || || ||||| || ||||||||||||||||||||||| || ||||| |  |      
-------------------------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtggccaactatttaagtgctgaa---ggaatt--tggttgtgtttcctgatgcagGG----GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtatatttt--gttctttt--atttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttag---tgaatattgaatatggtactgatcct----ctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
                    |||  ||||   ||  |||  | ||   |        |||     |||||    |     |   |  || |  | |     |||     |  ||||    |||  | ||| || |     || |||  | |||| ||||| |  | || || ||||| || |||   | ||| |||  | |||| |  || |||||||| |||||||||||||||||||||||  | | |||    |
gtatatctacttctgttctggtagcttttcaatttgtttgcacttctgttgttctttcaatcaagaccttattgttgatattcaggcttttccttttccctgttccctttccatatcagttattat-ctggtcataatgtttctttctaattgc-agGTTACCACACGGTCACCAAAAGATGGAATATGTTATAAGAAGTTGCCAAGATCAAGTGCTATTAAGGTGATTGATTTTGGTAGCACAGCTTTTGAGTGTC

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|45568628|gb|CK986157.1|CK986157
EST:     CCTTGTTTCTCCGGAGTACATTAAAGTGCCTGAATACAAA                         GTCTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
genomic: CCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
EST: gi|71434755|gb|DR815805.1|DR815805
EST:     AGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA                         GTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
genomic: AGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
                           tactgat  putative branch site (score: 2)
                                 tcctctttttttcatt  CT-rich tract
           tgaatattgaatat  TA-rich tract