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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

Basic information

species Glycine max
transcript GLYMA10G02400.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                                                       | || | | |||  ||  |  ||||       | |  | |   |  ||   || ||||       |  |   || |    ||    ||   ||   ||||||| || || ||||| |||||||||||||  ||||| || |||||||| ||||| | ||| ||||| ||||| ||||||||||||||||| || ||||
-------------------------------------------------------gttactctccat--ctcatcatattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 20
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                                       | |||  || | |||  |     |||||  ||    || |      ||| |     | || | || |||| || ||   |    | |    | ||  |  ||   |||   |||||| | | |||||||||||||||||| ||   |||||||||||||||||| || ||    || || || ||||| ||||| || ||||| || || ||||
---------------------------------------cttcaccttctctggtcaa----tgcatgcctgaacgtgt------agtgttgcagcattat-atcttttaaaatgcatggagcttatgaatcttgctataacaattt---cagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATACCCCCGGACGAAATAGGTGTCACCTTTGAGGACATTGGGGCATTGGAAA

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 5
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                                                              | || | || |   ||||    |   ||||       || |||  |  | ||    | |    ||   |||   |  |    ||||  |||||||| || || |||||||| ||||||||||  ||| | || |||||||| || |||| ||| ||||| || || ||||||||||||||||| || || |
-------------------------------------------------------------gtacact-ctcccaatattgtcatgagttctg------gtgattcctcaagttagttgctgaatactc-tatgtataaatcctttttctcagGATGTTGTCACAGAGAATGAGTTTGAGAAAAGGCTTTTGGCAGATGTTATACCTCCAAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                                                                   ||| |      | ||| | |      |   | || |||  | || || |    |   |||   || |          ||||  |||||||| || || |||||||||||||||||||  ||| | |  |||||||| ||||| | ||| ||||| || || ||||||||||||||||| || || |
------------------------------------------------------------------gtacaatcccc-tacatattgccgtgctttttggtgattcctcgagttatttactgaacactc-tacttacaagtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                                                                      || |  |||  |  |  ||    ||  ||| |      | || |   ||||| | ||   |||| |  |   | || || |||||||| ||||| ||||||||||| ||||||||||| ||  | || || ||||| |||| |||||| || ||  | ||   ||||||||| ||||| ||||
---------------------------------------------------------------------gtaattatatagaaatc-ttatgctattttgactccaaattaacttctggattttaacaattattat--gctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 19
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                                                               | | || || || || | |  |  ||||||  ||  |     |  | | ||  || |||   |  ||  ||  |     |  | || |||||||| ||||||||||| |||||||||||||||||  |  | ||||| |||||||| |  ||||| || ||  | |||||||||||||||||| | ||||
---------------------------------------------------------------gtaatatta-tgttacttaatttctttcttc-ccaagctgcctagtaagttccgg-attaagagttggtttacta----tactgtttcagGATGTTGTTACTGAGAACGAATTTGAGAAAAAACTGTTGTCGGATGTCATTCCACCTAGCGATATAGGTGTTTCCTTTGATGATATTGGAGCTCTGGAAA

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                      ||| ||  |  | | || || |   ||  |||   |||| |  |  |  |     |   ||  |     | ||    || ||||  | |  ||| |||     |  | ||| |    |     |||| |||||||||||||||||||||||||||||||| ||||||||| | |||||||||||||| | ||||||||| || || |||||||||||||||||||||||||
--------------------gtaaagttgcagatgtctctataaa--ttcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttgga-----atttttatgccaaaa-----tttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA

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|192316675|gb|FK009360.1|FK009360
EST:     TTCTACAGGGCATTCAAAATGAGAACAAAAACTTGAAAAAATCACTGAAG                         GATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATT
genomic: TTCTACAGGGCATTCAAAATGAGAACAAAAACTTGAAAAAATCACTGAAGgtaatttaat ... gtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATT
EST: gi|207817720|gb|GD792677.1|GD792677
EST:     GAGAACAAAAACTTGAAAAAATCACTGAAG                         GATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATT
genomic: GAGAACAAAAACTTGAAAAAATCACTGAAGgtaatttaat ... gtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATT
EST: gi|24205782|gb|BU965035.1|BU965035
EST:     TTCTACAGGGCATTCAAAATGAGAACAAAAACTTGAAAAAATCACTGAAG                         GATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATT
genomic: TTCTACAGGGCATTCAAAATGAGAACAAAAACTTGAAAAAATCACTGAAGgtaatttaat ... gtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                                           ttgtttttcc  CT-rich tract
     ttttttgaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT