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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacatattttttaccatattatggctcgatgtctgatctgaaacacatttttttttttgtttaaaggttttgaactaagccagatctgtgtttgtttgttgttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC

Basic information

species Glycine max
transcript GLYMA08G01860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01860.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g44630.3 (Oryza sativa), 3'ss of exon 1
gtatacatattttttaccatattatggctcgatgtctgatctgaaacacatttttttttttgtttaaaggttttgaactaagccagatctgtgtttgtttgttgttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC
 ||||||   ||  | | |     || |  ||   |||| |    ||| |     |       |||| ||   |  |||||     |||  | | | ||   ||||  ||   |||| ||||||||||||||||| || || ||||| ||||| ||||| |||||||||||||| ||  ||||  | ||||||||  | ||||| || || || ||
-tatacagtcttacttcaac----tgtcatgacaactgacc----acaaaacaactacggcaattaagggcact--actaat----atccat-tatattgtctgttactgcaacagGAGGACACATCAACCCAGCAGTTACTTTTGGGCTGTTCTTGGCCAGGAAGCTGTCCCTGACCCGGGCCATCTTCTACATAGTGATGCAATGCCTAGGGGC

upper sequence: GLYMA08G01860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G392975_T01 (Zea mays), 3'ss of exon 2
gtatacatattttttaccatattatggctcgatgtctgatctgaaacacatttttttttttgtttaaaggttttgaactaagccag-atctgtgtttgtttgttgttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC
                ||||  |||    | | |  | | |  | | |||    |          || ||      || |  |||  |   ||  ||   || || ||      |||| |||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| || |||||  | ||||||||||||||||| || || || ||
------------gaacccatgctattcagcaaagcataaaccaata-acacgactacaagcaaccaagggcc----accacaccactaatggttgttacctgctgctgcaacaacagGAGGACACATCAACCCAGCTGTGACCTTCGGGCTGTTCTTGGCCAGGAAGCTGTCCCTGACTAGGGCCATCTTCTACATTATCATGCAATGCCTGGGTGC

upper sequence: GLYMA08G01860.1 (Glycine max), 3'ss of exon 1
lower sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 1
gtatacatattttttaccatattatggctcgatgtctgatctgaaacacatttttttttttgtt-taaaggttttgaactaagccag-atctgtgtttgtttgttgttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC
                    | | ||     ||   ||   |  | ||    |             ||        | | ||| ||  |    || |||||   || |  ||   |||| ||||||||||||||||||||||| || || ||||| || || |||||||||||||| || ||||| || |||||||| |||||||| || || || ||
------------------gaactgtgaaagaatccatgcaattcagcaagcatagaccaagaacacaactacaacaaccaaagacaccactaatggttgttacctgctactgcaacagGAGGACACATCAACCCAGCTGTGACTTTCGGGCTGTTCTTAGCCAGGAAGCTGTCCCTGACTAGGGCCCTCTTCTACATCATCATGCAATGCCTGGGTGC

upper sequence: GLYMA08G01860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G174807_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------gtatacatattttttaccatattatggctcgatgtctg----atctgaaacac--atttttttttttgtttaaaggttttgaactaagccag-------atctgtgtttgtttgttgttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC
                                               || |   | ||  |   | |    || ||||  || ||    | |||     |  || ||| | | | | |     | |    ||    |          ||| | | | | | || | |    |||||| || ||||||||||| || |||||||| || |||||  |||| |||||| ||||||| || |||||  |||| ||||| ||||||||||| || || ||
gtaccgtacacgccgcccgcccggccgcctctttggcttcgtcctctgtttctttcttcctctgcttgccttgcctcgtcgtttgtgcaaactggtttgctgatgtttctctctctctctctctctctctctctctctctctctctctctctctctctctcttctcgcaactgcagGCGGGCACATCAACCCGGCGGTGACCTTCGGGCTGTTCCTGGCGAGGAAGTTGTCCCTCACCAGGGCGGTGTTTTACATCATCATGCAGTGCCTGGGCGC

upper sequence: GLYMA08G01860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G174807_T03 (Zea mays), 3'ss of exon 1
gtatacatattttttaccatattatggctcgatgtctgatctgaaacacatttttttttttgtttaaaggttttgaactaagccagatctgtgtttgtttgttgttgt-tgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAA-CAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC-
               ||   |    ||| |     |    | |  ||        | ||       | |   |||  |    ||||  | |||||| |   |  |  |    |||  |||  | ||||  |   || |    | |      |||    ||| ||  ||||| | |   ||| |||   |     ||   || ||  | | |  |   | 
-----------cgcaactgcaggcgggcacatcaacccggcggtgaccttcgggctgttcctggcgaggaagttgtccctcaccagggcggtgttt-tacatcatcatgcagTGCCTGGGCGC-CATCTGCGGCGCGGGCGTCGTCAAGGGGTTCC-AGCAGGG--GCTGTACATGGGCAACGGCGGCGGCGC-CAACGTCGTG--GCGCCCGGCTACA

upper sequence: GLYMA08G01860.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------gtatacatattttttaccatattatggctcgatgt-ctgatctgaaacacatttttttttttgtttaaaggttttgaactaagccagatctgtgttt----gtttgttg---------------ttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC
                              | |   ||  |||| |  |   |    |   ||   || ||| |       || ||  |||        | | ||   |   |    | ||| |||     | || ||               |||||||  |||| ||||||||||||||||||||||||||||||||| |  |||| ||||||||||| || || |||||| | |||||||| || |||||||| ||||| ||
gtgtgcaccactgctcttccttcctcagcctttctttagctttttctgttaaacactttactgggttgctctaagttcttcttcttcctttagccttctgatgtgggttgctcttagtgtgttttttagcatctgatggaagttttgtgtggtttgttgtctcagGAGGACACATCAACCCAGCTGTGACCTTTGGTCTGCTACTGGCGAGGAAGCTGTCTCTTACCAGGGCAATTTTCTACATCATAATGCAGTGCCTTGGTGC

upper sequence: GLYMA08G01860.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 1
gtatacatattttttaccatattatggctcgatgtctgatctgaaacacatttttttttttgtttaaaggttttgaactaagccagatctgtgtttgtttgttgttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC
          | | |||  | |||   ||       |   ||  | |||| |||| |        | |   |||   ||  |       | |  ||  ||| ||  |||   ||||| || ||||| |||||||| ||||| ||||| ||| | |||||||| ||||||||||||||  | ||  |||||||||| ||||||||||| || || ||
--------tctgtctactttcttacctctttccccatagcctcca-cacagttttctag------agaaagtttcctctgtgttgatcttatcatttgttgatgg-gtttgggcagGAGGGCACATAAACCCAGCGGTGACATTTGGGCTGCTCTTGGCAAGAAAGCTGTCCCTAACCCGAGCCGTGTTCTACATGATCATGCAGTGCCTGGGTGC

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|192297999|gb|FG988413.1|FG988413
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|22541360|gb|BU091203.1|BU091203
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|21678086|gb|BQ630437.1|BQ630437
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|213601267|gb|DB956533.1|DB956533
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|6072113|gb|AW101500.1|AW101500
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|15815682|gb|BI787957.1|BI787957
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|16105227|gb|BI892967.1|BI892967
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|11688058|gb|BF595734.1|BF595734
EST:     CTTTGGTGGCATGATCTATGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|26048790|gb|CA785243.1|CA785243
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|193703970|gb|FK647402.1|FK647402
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCCACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTCTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|213616646|gb|DB969170.1|DB969170
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAA                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|7042326|gb|AW472220.1|AW472220
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|6566507|gb|AW234152.1|AW234152
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|27423559|gb|CA935079.1|CA935079
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|13480718|gb|BG510061.1|BG510061
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|9820655|gb|BE556165.1|BE556165
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|14990914|gb|BI316587.1|BI316587
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|209713437|gb|BW679252.1|BW679252
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|192298833|gb|FG988654.1|FG988654
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|192330399|gb|FK022614.1|FK022614
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|193697084|gb|FK638898.1|FK638898
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCCACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTCTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
EST: gi|17400722|gb|BM177504.1|BM177504
EST:     CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAG                         GGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC
genomic: CTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATTTCAGgtatacatat ... gttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaaaggttttgaactaagccagatctgtgtttgtttgttgttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC
         ttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacatattttttaccatattatggctcgatgtctgatctgaaacacatttttttttttgtttaaaggttttgaactaagccagatctgtgtttgtttgttgttgttgttgcagGGGGACACATCAACCCAGCTGTGACCTTTGGTCTGTTTTTGGCAAGGAAGCTGTCCCTAACAAGGGCACTGTTCTACATTATCATGCAGTGTCTTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG