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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG

Basic information

species Glycine max
transcript GLYMA01G05080.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
                  | || ||||       ||||||| ||||  || | |         |||  |  | | | ||     |  || |||  |  ||||||||| |||||||||||||| || || ||  | || ||||| ||||||||||| |||||||| ||||| ||||| || ||||| |||
--------------tcttaactatatga----tggtactatcttctaatgccca---------cttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 2
---------ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
         |||  | ||   |||      |   |  |     ||||||| ||||  || | |         |||  |  | | | ||     |  || |||  |  ||||||||| |||||||||||||| || || ||  | || ||||| ||||||||||| |||||||| ||||| ||||| || ||||| |||
ctcctctggcttattctgatacaactctcttaactatatgatggtactatcttctaatgccca---------cttatatgtgtcaccctgacatttttctcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 5
ctttctatggatcaatg-aatctgtatggaaatc--agtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
| |  |   |||||    ||| | | | |   |         | |    |  ||    |   |    | |  | ||| ||  |  ||    | |   | | ||||||||| ||||||||||| || || |||||| |||||||||| |||||||| ||||||||||| ||||| |||||||| || || |||
catgatgatgatcatcataatgtttttagcttttttgaggaaactaaactaagtattattttgctgttgctggctctaagttctcttaatcttt---tgtcagTTTATGCGGATGGAAGCATTTGCTTAGACATTCTACAAAATCAGTGGAGTCCAATTTATGATGTAGCTGCCATACTTACATCCATCCAG

upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17802 (Selaginella moellendorffii), 3'ss of exon 3
ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattt-tagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
                               | ||| |  || |  ||| |         ||| || |  || |       | || ||  ||  |||  ||||||||| |||||||| || ||  | |||||  | |||||||||||||||||||| || |||||||| ||||| ||||| || || |||
------------------------------gtgagtccctttcttctttctt--------taattttctttttt-------tcttactcatctttttgcagTTTATGCTGATGGAAGTATTTGCCTCGACATACTGCAAAATCAATGGAGTCCGATCTACGATGTTGCGGCAATTCTTACGTCCATACAG

upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
                                                    ||||  | | | |   |||    | |  | || |    ||  |   ||||||||| ||||||||||| ||| | |||||  | |||||||| ||||| ||||| ||||||||||| |||||||| || || || |||
--------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctc--tcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG

upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23951 (Selaginella moellendorffii), 3'ss of exon 3
ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
                                                    ||||  | | | |   |||    | |  | || |    ||  |   ||||||||| ||||||||||| ||| | |||||  | |||||||| ||||| ||||||||||||||||| |||||||| || || || |||
--------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgcgctc--tcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATTTATGATGTTGCCGCAATACTGACATCGATCCAG

upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16328 (Selaginella moellendorffii), 3'ss of exon 3
ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
                               | ||| |  |  |  ||| |    |   ||  ||||   |||| |  | | | || | |        ||||||||| |||||||| || ||  | |||||| | |||||||||||||||||||| || |||||||| ||||| ||||| || || |||
------------------------------gtgagtcccttgcttctttct----ttgagtttcttctttttctta--ctcatctcttcgc-------agTTTATGCTGATGGAAGTATTTGCCTCGACATTCTGCAAAATCAATGGAGTCCGATCTACGATGTTGCGGCAATTCTTACGTCCATACAG

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|22933973|gb|BU551112.1|BU551112
EST:     TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACA                         TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
genomic: TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACAgtaagtagga ... tcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
EST: gi|14126011|gb|BG790449.1|BG790449
EST:     TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACA                         TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
genomic: TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACAgtaagtagga ... tcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
EST: gi|19452681|gb|BM954091.1|BM954091
EST:     TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACA                         TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
genomic: TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACAgtaagtagga ... tcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
EST: gi|19452497|gb|BM953907.1|BM953907
EST:     TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACA                         TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
genomic: TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACAgtaagtagga ... tcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
EST: gi|151402063|gb|EV271876.1|EV271876
EST:     TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACA                         TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
genomic: TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACAgtaagtagga ... tcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
EST: gi|19348294|gb|BM892826.1|BM892826
EST:     TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACA                         TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
genomic: TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACAgtaagtagga ... tcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
EST: gi|11273919|gb|BF324308.1|BF324308
EST:     TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACA                         TTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC
genomic: TAATAAACCACCAGCAGTGCGCTTTGTTTCTCAAATGTTTCATCCAAACAgtaagtagga ... tcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG
            aggtaac  putative branch site (score: 3)
                                ccccttttccttgtca  putative PPT
                                             tcaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - caatgaa
- - - - - - - - - - -tgtatgg
- - - - - - - - - - - - - - - - - - - - - - - - tgtcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgag