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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgaggggttagattcacacttatttgcaaagtccccctttcatgcatactgttggttgagactgttctataatagcttgacttatttaatattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG

Basic information

species Glycine max
transcript GLYMA02G38160.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7
gatgaggggttagattcacacttatttgcaaagtccccctttcatgcatactgttggttgagactg---ttcta-taata-gcttgacttatttaatattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG
    |     |||  | |   ||  ||||    |  | ||||||    |    ||  || |   ||   ||||  | | | |||||| ||  |   | | | ||| ||||||||||||| || |||||||||||||| || || ||||| ||||| ||||| ||||| || |||||||| ||||  ||  | || |||
----attatctaggat-atttttcattgcctcatatctctttcaattgtgaaattatttcaagatgaatttctgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG

upper sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 7
gatgaggggttagattcacacttatttgcaaagtccccctttcatgc-atactgttggttgagac--tgttctataata-gcttgacttatttaatattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG-------
    |   || |   |||    | |||| |  ||   | | |  ||  ||         | | ||  |  | | |  || |||| | ||  |   |||    ||||||||||||| || || |||||||||||||| || ||  |||||||||| ||||| |||||||| || ||||||||||  ||| | || |||       
----atttgtcactgtcatttctctttgtatggtaaacatattttgagatgaatcacactaacaccttactttctcctatgcttcatttgctacctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAGGCAAGGT

upper sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G135283_T03 (Zea mays), 3'ss of exon 7
gatgaggggttagattcacacttatttgcaaagtccccctttcatgc-atactgttggttgagac--tgttctataata-gcttgacttatttaatattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG
    |   || |   |||    | |||| |  ||   | | |  ||  ||         | | ||  |  | | |  || |||| | ||  |   |||    ||||||||||||| || || |||||||||||||| || ||  |||||||||| ||||| |||||||| || ||||||||||  ||| | || |||
----atttgtcactgtcatttctctttgtatggtaaacatattttgagatgaatcacactaacaccttactttctcctatgcttcatttgctacctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAG

upper sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------------------gatgaggggttag---attcacacttatt-tgcaaagtccccctttcatgcatactgttggttg--agactgttctataatagcttgacttatttaata-ttcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG
                                                                   |||  ||| |||    || ||  ||| |  |  |  || |   | | | | |        |||   | ||     | || |   |||  | ||  |||| || |||| | || || ||||| || ||||| || || ||| | || ||||| ||||| |||||||||||||| || ||||| ||||||||| |||| |||
gttggttagttcatagccagcttagcttaatgcttcaacattctatctttatccaatataccattgagatatgggtttaatacatacaagcttttcgtttacggttcttatgttaagtaattgaacagtttttaaaccaaagtttatttatttg--tgatacaataatttgcagCTAGAAAAGAGTGCCGTGCTTTTCAGACCGAAACTTATTGTTGCGGGTGCAAGTGCTTATGCTCGTCTATATGACTATGCACGTATTCGTAAG

upper sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 7
gatgaggggttagattcacacttatttgcaaagtccccctttcatgcatactgttggttgagactgttctataat--agcttgacttatttaa-------tattc---gcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG
              | ||   || |||  ||||       || |||| ||          | | |    || |||  |  |||||||  | ||       |||||   |||||||||||||||||| |  || || || |||||| |||| |||||||| || ||||| ||||| || |||||||||||||||||| | ||||||
------------tttccaattttgtttataaagagttgactttatgcctatcaaacaaataaaataaaataaaatgaaagttgactttgtgaaataaaaatattcattgcagTTGGAGAAAAGTGCTGCCCTCTTCAGACCAAAACTAATTGTTGCTGGCGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAG

upper sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S51_296V6.1 (Physcomitrella patens), 3'ss of exon 4
-gatgaggggttagattcacacttatttgcaaagtccccctttcatgcatactgttggttgagactgttctataatagcttgacttatttaatattcgc----agTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG
   | |    ||| || ||    |  || |    ||  | | |  | |  | |    | ||| | ||| |   | |   ||||   |  ||| |||  |    |||||||||||| |||| | ||||| ||||||||| | ||||| |||||| ||||||| |||||||||| ||| || ||  |  || |  | |||
cttttaaatattaaatgcagcaatgcttac----tcgtcttgttttcctcaatccatgatgaaattgtgcatcagtta-ttgaaaaaaataacatttacgttcagTTGGAGAAAAATGCATTTCTTTTCAGGCCAAAACTGATAGTAGCTGGTTCTAGTGCCTATGCTCGCCATTACGACTACACTGGTATGAGTAAG

upper sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------------------------gatgaggggtt-agattcacacttatttgcaa--agtccccctttcatgcatac-tgttg--gttgagactgttctataatagcttgacttatttaatattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG
                                                                                        |||| |   || ||  |      ||  |   |  | || || |||| |  | |   ||||  |||| || | |  | ||| || |  | ||     | ||| |||| |||||||||| ||||| ||||  ||||||||||| ||||| |||||||| ||||| |||||||||| ||| || ||||| ||| | ||||||
gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaacagatcaatttg---gaaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG

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|5819930|gb|AI988197.1|AI988197
EST:     CAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG                         TTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCT
genomic: CAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAGgtaggtaggt ... atattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatactgttggttgagactgttctataatagcttgacttatttaatattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG
                                        atttaat  putative branch site (score: 4)
                                 ttgacttatttaatat  TA-rich tract