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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG

Basic information

species Glycine max
transcript GLYMA13G05700.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 4
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacat--ttacctccttgtgattaataaatca----aggataa-actgttgttt-ttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                              ||| || || || || || |||||||     || |||| ||  |  || |  | |||     ||||  |      |  |||  | | | |||  ||  ||||| |||||||| ||||| ||||||||||| || || ||||| ||||||||||| || ||  | |||||||| || ||||| |||||||| ||||||||||
----------------------------------------------gtttttttttttttttttgtatcactg----tgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 4
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttct-gagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                            || || ||  ||| | | | | |  |   ||||| |   ||||||||  |     || |  ||| || |       ||   || |   |||  ||||| |||||||| ||||| ||||||||||| || || ||||| ||||||||||| || ||  | |||||||| || ||||| |||||||| |||||||| |
------------------------------------------gtattttttttgtatcactgtgagactatatcttcttgctcctttacatgcaatattttttc-ttattata------gtattatggtcccttt-gcagGTGATCTCTGGTAAATTATATGCTGGACCCGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGACG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                 ||||  | || |  | |||   ||||||| |   ||   |    ||     || | | || ||   | |   |  |   ||||   |    | |   |||    |||| || ||||| ||| | |||||||| || ||||| ||||| ||||| |||||||| ||| | ||||||||||| ||||| || ||||| |||||||| |
--------------------------------gtatttatcttga-atgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttt---tcaa---ttccttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                              | || ||||| ||| || | | | | ||  |  | |||   |  |||      |||| |   ||  | |  |  || ||| ||   |  |         | |||  ||||| || ||||| ||| | ||||||||||| || || ||||| ||||| ||||| || ||| | ||||||||||| ||||| |||||||| ||||||||||
------------------------------gtattttattcttattgctgtgagt-ttgctgatctatttttttttcct---ttttaga---acaccatgtttcttgatacatagtgagtgt-------tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 4
gtttgtaaataattaaattgtaacggaataggatattattattaatgttat-tattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgt-ttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                             | | || ||  || |||   |  |  |  | |    |   || ||||||| |   |    ||   |   || |  |   ||||  | |||||  |||| || ||||| ||| | |||||||| || ||||| || |||||||||||||| || ||| | ||||||||||| ||||||||||| || ||||| ||||
--------------------------------------------gtatcatctagcataatttacaattagcgtccttcatgg--ttgcatttacatatata-acttgccatgacacgttt---ctgtcttattttcttagGTCATATCTGGTAAACTATATGCTGGTCCTGAAGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatca-aggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                            || | | |   || ||  || |    ||| |  |  |   || ||  || |         |||| |  ||   |  ||   |      |   ||  || || ||||   ||||| || ||||| ||| | ||||||||||| ||||| ||||| ||||||||||| || ||| | ||||||||| | ||||| ||||| || |||||||| |
---------------------------gtaagctttctataatag-gtcaaagatataaagaggac-ccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttac-ctccttgtgattaataaatcaaggataaa--ctgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                                  | | |  | | |         ||  |  |  |   || | |||  ||  ||   | | |||  | |  |   |   || |   || |  ||||| || || || || || |||||||| || |||||||||||||||||||||||||| ||  | || |||||||||||||| || ||||| ||||||||||
-------------------------------------------------gtaagtgct-tcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
gtttgtaaataattaaattgtaacggaataggatattatt-attaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                              | ||||  || | ||| |||| |   ||| || ||        || | || |||| |   |       ||| ||| |     |||          |  |  || |   ||||||| || || ||||| ||||||||||| ||||||||||| ||||| || || || || || || |||||  | || || |||||||||||||||||||
------------------------------gtatatagtttagtaaagttactga-attgttttt-------cacctatgtgactatgtctcgtttctcttatgagtgtcttatctc-------ttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17922 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                                           | | |||||||  |    | ||  ||  |||   |    | || |||  ||| |             || |   |||||||| || || || ||  | |||||||||||||||||||| || ||||||||||| || ||  |||| || |||||||||||||  ||||| ||||| || |
----------------------------------------------------------gtcagtatatcagga----taagttttgtcataggc----tcgtcattc-taagttg--------tctttctcaatcacagGTGATTTCCGGTAAGCTCTATGCTGGACCAGAAGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ10631 (Selaginella moellendorffii), 3'ss of exon 4
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                                                                         |   | ||    |  ||  |   || || |  | |  ||   ||||  |||| ||||| |||||  | ||||| ||||||||||| ||||| |||||||||||||| || || || || ||||| ||||| | | | |||||||| || |
----------------------------------------------------------------------------------------gtaagcttcgacattcttttttcctctagaa--agccttttcctttc--agGTGATCTCGGGAAAGCTTTATGCAGGACCAGAAGTGGATGTATGGAGCTGTGGTGTCATATTGTACGCACTTCTGTGTGGAAGTTTACCTTTTGACGACG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35371 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                                                                         |   | ||    |  ||  |   || || |  | |  ||   ||||  |||| ||||| |||||  | ||||| ||||||||||| ||||| |||||||||||||| || || || || ||||| ||||| | | | |||||||| || |
----------------------------------------------------------------------------------------gtaagcttcgactttcttttttcctctagaa--agccttttcctttc--agGTGATCTCGGGAAAGCTTTATGCAGGACCAGAAGTGGATGTATGGAGCTGTGGTGTCATATTGTACGCACTTCTGTGTGGAAGTTTACCTTTTGACGACG

upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                                                           | | ||||||| ||      |   |||    |||    || || |||  ||| |             || |   |||||||| || || || ||  | |||||||||||||||||||| || ||||||||||| || ||  |||| || |||||||||||||  ||||| ||||| || |
----------------------------------------------------------gtcagtatatcagtat-----aagttttg---ttataggctcgtcattc-taagttg--------tctttctcaatcacagGTGATTTCCGGTAAGCTCTATGCTGGACCAGAAGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACG

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|254330248|gb|GR841513.1|GR841513
EST:     GTCACTTTCTTAAGACAAGTTGTGGAAGCCCTAATTATGCGGCTCCAGAG                         GTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGT
genomic: GTCACTTTCTTAAGACAAGTTGTGGAAGCCCTAATTATGCGGCTCCAGAGgtttgtaaat ... tttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGT
EST: gi|193581741|gb|FK533110.1|FK533110
EST:     GTCACTTTCTTAAGACAAGTTGTGGAAGCCCTAATTATGCGGCTCCAGAG                         GTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAG
genomic: GTCACTTTCTTAAGACAAGTTGTGGAAGCCCTAATTATGCGGCTCCAGAGgtttgtaaat ... tttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAG
EST: gi|193571724|gb|FK527733.1|FK527733
EST:     GTCACTTTCTTAAGACAAGTTGTGGAAGCCCTAATTATGCGGCTCCAGAG                         GTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGANCTGT
genomic: GTCACTTTCTTAAGACAAGTTGTGGAAGCCCTAATTATGCGGCTCCAGAGgtttgtaaat ... tttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG
                  gattaat  putative branch site (score: 3)
                                          ttgtttttc  putative PPT
              ttgtgattaataaat  TA-rich tract