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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagcctcattttttttacactctcttttgttgtttttttgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC

Basic information

species Zea mays
transcript GRMZM2G171354_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
-----gtatgagcctcattttttttacactctcttttgt-tgtttttttgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
     || |    |||| ||   | | |  | |  |  | ||||  ||| ||||  |  | ||   |     | ||   | | ||||| ||||| ||||||||||||||||||||||||||||| || |||||  ||||||||||||||||||||||||| || || ||||| ||  |||||||||
gtactgtcttctactcaattcgctgataagcacagtactgtgttaattttcttgctaacttttttttcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------gtatgagcctcatttttt-ttacactctcttttgttgtttttttgc--ttggaatatattg--ggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                                                |   ||  |  |   || || ||   ||   || || | |  |    |  ||||  |     | ||  ||| ||     | |||||||| | ||||||||||||| | |||||||| || || ||  ||||  | |||| |||||| ||||| ||||| ||||||||||| ||  | ||||| |
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 5
-------------------------gtatgagcctcattttttttacactctcttttgttgtttttttgcttggaatatattgggtta-atttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                         ||   ||  |    || || |     |||    || || || || |     | |  |    || |  |||| | | | |||||  |||  | |||||||||  ||||||||||||| |||||   ||| || |||||||| ||||| || ||||||||||||||||||||  | |||||| 
gtatgtgactttagtcataattattgtggtagtttttaattcttcatggcttctggacttattgttctggt--atctgttctaacctataaatgtttc-tgtgcagACATTATGTCGAATGTTTATAATCAATGCTGGTCCCGGTTTTAAGCTGCTTTGGAACACGGTGAAATCATTTCTTGATCCCAAAACTACTTCAAAGATAA

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 4
-----------gtatgagcctcattttttttac-actctcttttgttgtttttttgcttggaata--tattgggt-taattt----gttgcatc-tccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
            | | | | ||| |||||||   |||      |||| || || | | || | |   | |||  | |||| |     |   | | | ||||| || | ||||||||||||  | ||||||||||| |||||   | |||| |||||||| |||||  | ||||||||||||||||||||  | ||||| |
caagtatgtagttttaatcatcactttttttctgacttcagaatgttcttattgttcatgtagtgcttcttgattctaatctctaaatgataccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATACTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------gtatgagcctcatttttt-ttacactctcttttgttgtttt--tttgcttggaatatattg--ggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                                                     |    |  |  |   || || ||   ||    | || | |  | || |   | |  | ||  | ||  ||| ||     | |||||||| | ||||||||||||| | |||||||| || || ||  ||||  | ||||||||||| ||||| ||||| ||||||||||| ||  | ||||| |
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------gtatgagcctcattttttttacac-----tctcttttgttgttt----ttttgct--tggaatatattgggttaatttgttgcatc-tccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                                                                   |||||   | |   |||||| |      | | |  |   || |    | |||||  |    ||| ||   ||  ||| ||  ||  | |||||||| | ||||||||||||  | |||||||| || || ||  || | |||||||||||||| ||||| || ||||||||||| || ||  | ||||| |
gtgtgtaacactgtcggtttctgtgtattttgttacattacgccccttgttttgatttcatcggttatatgaaattaaaagtttttaaagaagaatatgtactaaggtctcaactattgctgattttttattttttatttctttttttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 5
-----------------gtatgagcctcattttttttacactctct---tttgttgtttttttgct-tggaatatattgggttaatttgttgcatctc--cagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                   || |   |  |  ||||||     |||   ||| | |  || ||| | ||| || | ||        |   ||  |||   |||||  |||  | |||||||||  ||||||||||||| |||||   ||| || |||||||| ||||| || ||||||||||||||||||||  | |||||| 
gtatgtgactttagtcataattattgtggtagtttttagttcttctaggtttctggacttattgttctggtatctgttctaacctataaatgattctgtgcagACATTATGTCGAATGTTTATAATCAATGCTGGTCCCGGTTTTAAGCTGCTTTGGAACACAGTGAAATCATTTCTTGATCCCAAAACTACTTCAAAGATAA

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------gtatgagcctcattttttttacactctcttttgtt---gtttttttgcttggaatatattgggttaatttgttgcatctc-------cagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                                                         || ||   | |  || |  | |    | | |  |   || |      ||      |||||  ||  | | |  | |||        |||||||| | ||||||||||||  | |||||||| ||||| ||  || | |||||||||||||| ||||| || |||||||||||||| ||  | ||||| |
gtgagtaacactgccggtttctgtgtattatggcccttattttgatttcatccgatataggaaattaaaattgtaaagaagaacatgtactaaggtctcaactttttctgattattgatttgttatttctcttcttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGACCGGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAAACAACTTCAAAGATTC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 5
-----------gtatgagcctcattttttttacactctc----ttttgttgtttttt------tgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
            | | | | ||| |||||||      ||    |||| || || ||       |||||  ||  | |    |  |  || | |   | ||||| || | ||||||||||||  | ||||||||||| |||||   | | || |||||||| |||||  | ||||||||||||||||||||  | ||||| |
caagtatattgttttaatcatcactttttttctgacttcagaattttcttattgttcatgtagtgcttctaagttctaatatctaaatgatac-cgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgagcctcattttttttacactctcttttgttgtttttttgcttggaatatattgggttaatttgttgcatctc---cagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
      |  | | ||  ||    ||     |  ||| | |   |  |  |||        |   ||||| | || ||   ||||||||  |||||||||||||| ||||||| || || || ||  ||||||| ||||||||||| |||  ||||||||| || || ||  | || || || |
------gtattagttaattggagcttctaatacttgatctcaggtatcaaatgctaatcttggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------gtatgagcctcattttttttacactctcttttgttgtttttttgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                                                                         || ||       ||   |  || |        |   | || | ||       |||    || |    |    ||| ||||| || | ||||||||||||  | ||||||||||| |||||  |||| || |||||||| |||||| | ||||||||||| ||||| ||  ||||||| |
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagttgaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC

upper sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------gtatgagcctcattttttttacactctcttttgttgtttttttgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                                |||     | ||   ||| | | |   | | | ||  |   |   ||   |  ||   |     |  |  |  || |||||||| | ||||||||||||| ||||||||||||| || ||  |||| || ||||||||||| ||| | ||||| ||||||||||| ||  ||||||| |
gtattcaacctttttctgttgacatgataagctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctggatcttgaactctcttaactgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTCTGGAACACTGTAAAGACTTTTCTAGATCCCAAAACAACTTCCAAGATTC

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|160481336|gb|EY254270.1|EY254270
EST:     GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAG                         ACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
genomic: GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAGgtatgagcct ... gcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
EST: gi|32933167|gb|CF037979.1|CF037979
EST:     GTGAATTAATTCGGCGACTGCAGAAAATTGACAATGATAACTACCCAGAG                         ACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
genomic: GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAGgtatgagcct ... gcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
EST: gi|211297306|gb|FK975033.1|FK975033
EST:     GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAG                         ACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
genomic: GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAGgtatgagcct ... gcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
EST: gi|13178166|gb|BG349424.1|BG349424
EST:     GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAG                         ACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTC
genomic: GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAGgtatgagcct ... gcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTC
EST: gi|6564181|gb|AW231803.1|AW231803
EST:     GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAG                         ACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
genomic: GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAGgtatgagcct ... gcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
EST: gi|211297305|gb|FK975032.1|FK975032
EST:     GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAG                         ACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA
genomic: GTGAATTAATTCAGCGACTGCAGAAAATTGACAATGATAACTACCCAGAGgtatgagcct ... gcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttttgttgtttttttgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
                                 ggttaat  putative branch site (score: 4)
                                              catctcc  putative PPT
        ttgttttttt  TA-rich tract