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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

Basic information

species Glycine max
transcript GLYMA09G41330.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
------gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
       ||  |    | |   | ||| ||| ||   | | |   |  || |  || | |||  |  |   |   |   |   || ||   ||     ||||||| |||||||||||||||||||||||||||||||| || || || ||  | || ||||| ||||| ||||| ||||||||||||||||||
gtaactatttcaagcttgcttgattttcatctgtgcatgtgcctac--caaatacattctgtaattgtacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
------gttcaacatctccaaaaattttatcagt-----tgttttccactct-acagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
       ||  |    |    || ||| ||| ||     ||  | ||| | | |       || ||||    |    ||||   | ||| |  ||| |      |||| || |||||||||||||||||||| ||||||||||| || || || ||  | || ||||| ||||| ||||| ||||||||||||||||||
gtaactatttcaggcttgattaattttcatctgtgcaaatgcctaccattttcattctgtaagattgtacctaaatgtttaactcatttgcactatacc-----agGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
    ||   | |   |  |   |||| ||  ||   | |           ||   || | ||  ||    |        |  |   || |  ||||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| || ||||| |||
--gtaatgccactctagctcacatcaattcattcagatt-------gattgtccttgcttat--atcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
    ||| | | || |  || | |   |||   |   || |     | || | |||        ||   || ||   |   | ||||     ||||||||||||||||||| |||||||||||||||||||||||||| || ||| | |||||||| ||||| ||||| |||||||| |||||||||
--gtaactttttcatac-ttgtgtacattgacctgttctttg----aacaatatgtac------atcagttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
             |   |||||   | | || | |   |||  ||          |  |  |  ||   |  ||   |   | ||||     |||| |||||||||||||| |||||||||||||||||||| ||||| || ||| | |||||||| ||||||||||| |||||||| |||||||||
-----------gtagctattttcatactcgtgtacagatctg-agctttgaacaat--ttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
|| |||  |||  |||  ||||  |   | |    || | |          ||||     | | | |   | |  ||  |  || ||||   ||||||| ||||||||||| ||||| || |||||||||||||| ||||| ||  ||||||| |||||||| || || || | |||||||||||||
gtacaatttctttaaaccttttccc---tatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc---agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------gttcaacatctccaaaaattttatcagttgttttccactcta--cagaagcagtttgtggtcattga-tttattccttt--ttctttattctgcttt--agGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
                                           |||   ||| |  |      | | || ||  | |  | | |   | |||| |     |    ||  | | || |  |    ||  | |||    |||  ||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| | ||||| |||||||| || || ||| ||||||||||||||
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------gttcaacatctccaaaaatt-ttat-cagttgttttccactctacagaagcagt-ttgtggtcattgatttattcctttttctttattctgc--tttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
                             |   |  |  ||||    | |||| |  || || |||    |       || | || |  |  |  ||| | | || ||| |||||| ||   | ||||||||||||||||||||||| |||||||| |||||||| || ||||||||  | ||||| || ||||| ||||| |||||||| || || || 
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttt-tttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
                             || |        ||  || ||  |||||||| |    | |  | |  |    |          ||||||||||||| ||||||||||||||||| ||||| || |||||||| ||  || | ||||| || || ||  | || |||   |||||||| 
-----------------------------gtatgaag----acgaaaacacattgtggtc-tgagctcaaacttagtaacgtccgtgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

upper sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
gttcaacatctccaaaaattttatcagttgttttccactctacagaag-cagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
                                    |      ||||  ||  |||||||| |    | |  | |  |    |          ||||||||||||| ||||||||||||||||| || || || |||||||| ||  || | ||||| || || ||  | || |||   |||||||| 
----------------------------------gtatgaagaagaaaacacattgtggtc-tgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

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|254336235|gb|GR842414.1|GR842414
EST:     TATGCTAGAATTATCCAAAAGCTTGGTTTCCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
genomic: TATGCTAGAATTATTCAAAAGCTTGGTTTCCCAGCTAAATTTAAGgttcaacatc ... tctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
EST: gi|254334604|gb|GR844389.1|GR844389
EST:     TATGCTAGAATTATTCAAAAGCTTGGTTTCCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
genomic: TATGCTAGAATTATTCAAAAGCTTGGTTTCCCAGCTAAATTTAAGgttcaacatc ... tctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
EST: gi|19270744|gb|BM887000.1|BM887000
EST:     TATGCTAGAATTATCCAAAAGCTTGGTTTCCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
genomic: TATGCTAGAATTATTCAAAAGCTTGGTTTCCCAGCTAAATTTAAGgttcaacatc ... tctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
EST: gi|21887668|gb|BQ740881.1|BQ740881
EST:     TATGCTAGAATTATCCAAAAGCTTGGTTTCCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
genomic: TATGCTAGAATTATTCAAAAGCTTGGTTTCCCAGCTAAATTTAAGgttcaacatc ... tctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
EST: gi|254334605|gb|GR844390.1|GR844390
EST:     TATGCTAGAATTATTCAAAAGCTTGGTTTCCCAGCTAAATTTAAG                         GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT
genomic: TATGCTAGAATTATTCAAAAGCTTGGTTTCCCAGCTAAATTTAAGgttcaacatc ... tctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
                    cattgat  putative branch site (score: 4)
                          tttattcctttttctt  CT-rich tract
                         atttattcctttttct  TA-rich tract