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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgctctcctaacatttttcagacttgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA

Basic information

species Glycine max
transcript GLYMA06G42830.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g35540.1 (Oryza sativa), 3'ss of exon 4
gtattttgctctcctaacatttttcagact-tgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA
               || | ||  ||  || || | |  ||||   |   |     ||    || ||  ||  | | | || || | |||  ||  ||| || |||   | |   ||   |||||||||||||||||||| |||||| |||||||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||| |||   ||| 
-----------atgaaaaacttcccattctctggtctggaggtttgtgcct-----tg----ttgacaggttgttttt-gtttaca-tctaatttcatttatcatttcctttggtatcc-cagAATGCTCCAGATGGTTCATTCTTTTTGCTTCATGCTTGTGCGCATAATCCCACTGGAGTAGATCCTTCAGAAGAACAATGGAGGGAGATATCTCATCAGT

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g14110.1 (Oryza sativa), 3'ss of exon 4
gtattttgctctcctaacatttttcagacttgctttataggtcaattt-ttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA
                         | ||||  ||| |   ||| ||| ||| || ||   ||   ||  |  |   |   |||||      || |||| ||| ||  |  |  ||| | ||||| |||||| ||||||| |||||| |||||||||||||||| ||||||||||||||||| |||||| |||||||||||||||||||||| || | |||  
---------------------aggtacacttagtttttc--tcactttcttataggtgcttctgacctgttgatgggtttcctatagctccttttaatttatttttgttcctctcatctgcagAACGCTCCAAATGGTTCATTCTTTTTGCTTCATGCTTGTGCCCATAATCCTACTGGAGTTGATCCTACAGAAGAACAATGGAGAGAGATATCCTACCAAT

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 4
gtattttgctctcctaacatttttcagacttgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA
                  |   |      ||  ||| | | ||| |   |   |         | ||   | | |   ||||  ||| | |||   || ||  ||   | |  ||| | |||||||||||||||||||| |||||| |||||||||| |||||||||||||| || || ||||||||| | || |||||||||||||| || ||    ||| 
---------------ggaaccatgagagattattttgt-gctcagtgaatctggtctgctgagtgctgacaattt---gtctgaaat-tccttttgtttatgcttttctgt--catctgcagAATGCTCCAGATGGTTCATTCTTTTTGCTTCATGCATGTGCTCATAATCCCACCGGTGTAGATCCTACGGAGGAACAATGGAGAGAAATATCCCATCAGT

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 4
gtattttgctctcctaacatttttcagacttgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA
                             | ||   | ||  ||  || | ||  |  ||| |   |  ||||   |    | | | | || ||| |   |||    || || ||||    ||||||||| || || || ||||| || ||||||||||||||||||||||||||||||||||| ||| |||| ||||||||||||||||| ||    |   
---------------------------gttagc---aaagaacatcttcttcaact--agcatcttttttacttctt--cttgttaacatcctaattctgttaagcctttttccata----gAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g01820.t01 (Vitis vinifera), 3'ss of exon 4
gtattttgctct--cctaacatttttcagacttgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA
||| || |  |   |  |   |  |      ||  ||| |     | | |||| |  |   | ||| |  ||   || |  | |||    || || | ||| ||||| |||  |   |  ||||||||||||| |||| || |||||||| |||||||||||||||||||| ||||||||||| ||||||||||| |||||||||| ||||||||| | |||| 
gtacttaggccggactcattgtgatctgtgatttatttgtctcatactgttta-aacttctgttttccatgtttcctttcctttatttatttatttatttatttatttatttatttttg-acagAATGCTCCAAATGGATCATTCTTTCTACTTCATGCTTGTGCTCATAACCCTACTGGAGTGGATCCTTCAGAGGAACAATGGAAAGAGATCTCATACCAGT

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ37394 (Selaginella moellendorffii), 3'ss of exon 4
gtattttgctctcctaacatttttcagacttgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattatt-aattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA
                                                                    |||   | || | | |  |  |       | |  ||  || |  || ||   ||||| || || || || || ||| |  |||| ||||| |||||||||||||| |||||||| |||||| | |  || || |||| |||||| |||   |   
--------------------------------------------------------------------gtaagatctaatttttcgttcttcctttctgaaaatcgaacttgtaaatggccagAAAGCACCCGAGGGATCTTTCGTCTTGCTGCATGCGTGTGCTCATAATCCAACTGGAGTTGATCCTACTGCTGACCAGTGGAAAGAGATGTCTCAGCTCT

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ33874 (Selaginella moellendorffii), 3'ss of exon 4
gtattttgctctcctaacatttttcagacttgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA
                                                                  ||  | ||||   | | |  ||||| |   | ||     || |  || ||   ||||| || || || || || ||| |  |||| ||||| |||||||||||||| |||||||| |||||| | |  || || |||| |||||| |||   |   
-----------------------------------------------------------------gtaaga-tctaatttttttgttcttcctttctgaaaatcgaacttgtaaatggccagAAAGCACCCGAGGGATCTTTCGTCTTGCTGCATGCCTGTGCTCATAATCCAACTGGAGTTGATCCTACTGCTGACCAGTGGAAAGAGATGTCTCAGCTCT

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|19269530|gb|BM885786.1|BM885786
EST:     ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAG                         AATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
genomic: ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAGgtattttgct ... acatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
EST: gi|254345072|gb|GR851448.1|GR851448
EST:     ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAG                         AATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
genomic: ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAGgtattttgct ... acatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
EST: gi|6913336|gb|AW394866.1|AW394866
EST:     ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAG                         AATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
genomic: ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAGgtattttgct ... acatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
EST: gi|254336114|gb|GR841439.1|GR841439
EST:     ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAG                         AATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
genomic: ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAGgtattttgct ... acatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
EST: gi|37994754|gb|CF806351.1|CF806351
EST:     ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAG                         AATGCTCCAGA
genomic: ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAGgtattttgct ... acatatacagAATGCTCCAGA
EST: gi|9565855|gb|BE475364.1|BE475364
EST:     ACCCTGAGTCTAGAGGATTGGATTGTTCAGGACTGATGGATGACATAAAG                         AATGCTCCAGATGGTTGCTTCTTTCTGCTTCATGCTTGTGCTCATATTCCT
genomic: ACCCTGAGTCTAGAGGATTGGATTTTTCAGGACTGATGGATGACATAAAGgtattttgct ... acatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
EST: gi|254320419|gb|GR826868.1|GR826868
EST:     GGATGACATAAAG                         AATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT
genomic: GGATGACATAAAGgtattttgct ... acatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA
                                  tattaat  putative branch site (score: 2)
              tataatcttcttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttgctctcctaacatttttcagacttgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC