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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaccttcaccttcactattccatttgggcattttcttctgtctatttggtgacttctgtttccaaatcatggtcctgctttttttcccccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT

Basic information

species Glycine max
transcript GLYMA09G12420.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g42380.1 (Oryza sativa), 3'ss of exon 3
gtaaccttcaccttcactattccatttgggcattttcttctgtctatttggtgacttctgtttccaaa-----tcatggtcctgcttttttt-------cccccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
            || |||| |||     |  || ||    || ||  ||   || |||   |   |||     | | | | |||| | |  |       |  |  | | ||||||| || ||||||||||| ||||| |||||||| | ||| || ||| ||||||||||| |||| || || ||||| |||||||||||||  ||||||||
------------tttactagtcctggaagatatctttagatgcctggttctagagttcctctgttaaaactacttaggtttctgcatatcctcagtttgctacttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGGGTCGTATCATAGCTGGAACATGTCATAGTGCTAAGATGAACAGGACCAT

upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g52354.1 (Oryza sativa), 3'ss of exon 3
gtaaccttcaccttcactattccatttgggcattttc--ttctgtctatttggtgacttctgtttccaa-atcatggtcctgctttttttcccccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
 | ||   ||  || | |    ||| ||   |||            ||  || |    | |||||  |  ||        || ||   | |    |  | |||| ||||| ||||||||||||||||| |||||||| | |||||| ||  | ||  | ||| | || || || || |||||||| |||||||  || || ||
ttgactagcaatttaaat---tcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttccagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT

upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
gtaaccttcaccttcactattccatttgggcattttc--ttctgtctatttggtgacttctgtttccaa-atcatggtcctgctttttttcccccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
 | ||   ||  || | |    ||| ||   |||            ||  || |    | |||||  |  ||        || ||   | |    |  |  ||| ||||| ||||||||||||||||| |||||||| | |||||| ||  | ||  | ||| | || || || || |||||||| |||||||  || || ||
ttgactagcaatttaaat---tcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT

upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 3
gtaaccttcaccttcactattccatttgggcattttcttctgtctatttggtgacttctgtttcca--aatcatggtc-ctgctttttttcccccccat------acagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
              ||| | | ||     | ||| |  |  |     |  |      |||  | ||  |   ||| |  ||  ||   |||       |      ||||| || |||||||| ||||| |||||||||||||||| |||||| ||| |||| || ||| |||| || ||||| || ||||| |||||||  ||||||||
---------gttgacaccaattcagaaaagtattctaattggctagctaagctttaactgccttcatgagcgatgctgacttgttcccttcgttgttgtttggtaacagGTACTTATATTGATAAGAAATGCCCCTTCACTGGCACTGTTTCTATTAGGGGCCGCATCTTAGCTGGCACTTGCCATAGTGCCAAGATGATGAGGACCAT

upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: EDO96718 (Chlamydomonas reinhardtii), 3'ss of exon 2
----------------------------------------gtaacct---tcaccttcactattccatt-tgggcattttcttctgtctatttggtgacttctgtttccaaatcatggtcctgctttttttcccccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
                                         |||      |  |   ||   ||      |||||        | | |      |    ||  ||   |    ||    || |   |  ||| |  || | ||||    || || |||||||||||||||||||| ||||| || ||||| || || ||||||||  | |                                  
gtgcgtcccggggagctttgcgctaaacgtaatggagtaaataaatcgtgtggcaggcagggttgtgccgtgggcgccgcacgccggcagcgccgacgattgagtgcgcggtccaataaccaggcgtgcttcactgcc-tgcagGCCACTACATCGACAAGAAGTGCCCCTTCACCGGCAACGTGTCCATCCGTGGCCGTATCCTCACGG----------------------------------

upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S51_307V6.1 (Physcomitrella patens), 3'ss of exon 3
--gtaaccttcaccttcactattccatttgggcattttcttctgtctatttggtgacttctgtttccaaatcatggtcctgctttttttcccccccatac-agGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
  ||| || ||   ||   |   | |   |||  |    |||| |  |   | || ||  | |   ||   | |  |             ||||   ||  ||| ||||| || |||||||||||||||||||||||  ||||||| || || || || |||||  |||| |||    || |  |||| |||||  | || ||
tagtagccatcgagtttcgtgaccta---gggtttggatttctttgaaacggatgtctagtttcctcactccctaatttgaggaagggcacccctgctattagGTACATACATCGACAAGAAGTGCCCCTTCACTGGAGATGTTTCTATCCGAGGGCGCATCCTTACCGGAACTGTCAACTGCACTAAAATGACCCGTACGAT

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|192295631|gb|FG990485.1|FG990485
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|192327596|gb|FK020643.1|FK020643
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|213610237|gb|DB980823.1|DB980823
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|31474232|gb|CD416260.1|CD416260
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCTATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|298193555|gb|HO040203.1|HO040203
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAGGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|213612020|gb|DB964856.1|DB964856
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|151409325|gb|EV279133.1|EV279133
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|298192237|gb|HO036319.1|HO036319
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|192329280|gb|FK020199.1|FK020199
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|192323316|gb|FK017422.1|FK017422
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|10256428|gb|BE824194.1|BE824194
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|151410570|gb|EV280385.1|EV280385
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|192334757|gb|FK025262.1|FK025262
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|7145646|gb|AW507568.1|AW507568
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|38192824|gb|CF922030.1|CF922030
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|192327595|gb|FK020642.1|FK020642
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|38193079|gb|CF922285.1|CF922285
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|298185805|gb|HO030966.1|HO030966
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|151412049|gb|EV281861.1|EV281861
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|213610749|gb|DB963135.1|DB963135
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|192334069|gb|FK026226.1|FK026226
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
EST: gi|18040050|gb|BM308344.1|BM308344
EST:     TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAG                         GAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG
genomic: TTGGAAGTCAATTGGGCTTGGATTCAAGACTCCCAGAGATGCCATTGAAGgtaaatataa ... ccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggtgacttctgtttccaaatcatggtcctgctttttttcccccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT
                             tcctgctttttttccc  CT-rich tract
                                   ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccttcaccttcactattccatttgggcattttcttctgtctatttggtgacttctgtttccaaatcatggtcctgctttttttcccccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - -cttcacc
- - - - - - - - - - -ccatttg
- - - - - - - - - - - - - - ggcattt
- - - - - - - - - - - - - - - - - - -ttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - tggtgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttcc