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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggtgaaacaaattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA

Basic information

species Glycine max
transcript GLYMA19G34390.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G34390.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g40880.2 (Oryza sativa), 3'ss of exon 7
agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggtgaaacaaatt---cttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA--------------------------
                       || | ||  |   |  | |  |  |  | | |  ||   | ||||  | |  |   | | |||||||  ||   || ||||| ||||||||||  ||||||||||| ||||||||||| || ||||||||| |||| || ||||| || |  ||                          
---------------------gtgttaccagtttcactgtcaagtattctattacacata-acattgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCAGTGAGTTATCATTGCAGATCCAGAAT

upper sequence: GLYMA19G34390.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggtgaaacaaatt---cttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA
                       || | ||  |   |  | |  |  |  | | |  ||   | ||||  | |  |   | | |||||||  ||   || ||||| ||||||||||  ||||||||||| ||||||||||| || ||||||||| |||| || ||||| || |  ||
---------------------gtgttaccagtttcactgtcaagtattctattacacata-acattgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA

upper sequence: GLYMA19G34390.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggt---gaaacaaatt---cttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA
                       |||   | | |||| |||  ||     | |||||   | ||   | || ||  || |        |||||  ||    |  |||| ||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| || ||||| || |  ||
-----------------------gtatctaccagtgccctgcaatac--aaattcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA

upper sequence: GLYMA19G34390.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggtgaaacaaattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA
 |    || |     | | ||   |    | ||  | |     | | |||    ||||     |    |||| |   ||||       |||  | | ||||| ||||||||||| ||||||||||| ||||| |||||||| ||||||||||||||||||||||| | ||| ||
-gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaagttgggagacttac--aatagactctgattagtttt-------caagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA

upper sequence: GLYMA19G34390.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0141g00310.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------------------------agctgg--gatgcacagaaagaacagtaagcatctgtg-cactgacatga-----------tggagttcttatctgctttgttc-tgttgcattttggtga--aacaaattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA
                                                    | ||||  | |||| | |   | |  |     | | |  ||   | |  |           ||  || | |   | ||||  || | ||||||| || |||  || |  ||||  |||| |||||||||| |||||| ||||| ||||||||||| || ||||||||||||||||| ||| | | ||| ||
gtgagtagctattgatgttggctgcgtcattttattcttgttgagactttagaactggttggtgcataaacttatctttttttttttttttcaaaaataaaaaataaaaaatttgtggtacatgagtacttttctcatattgcattatgatgagcaatattttctgtagGGGTCAGTTTATGCACCATCGTTTGATCATGGTGTTGGAGATCCAGTTGAAGATGATATATTTATCAGCCTCCA

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|192331130|gb|FK020350.1|FK020350
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|192326255|gb|FK017617.1|FK017617
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|20815087|gb|BQ299565.1|BQ299565
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|151405354|gb|EV275168.1|EV275168
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|58020561|gb|CX707303.1|CX707303
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|58020732|gb|CX707474.1|CX707474
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|192325118|gb|FK019064.1|FK019064
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|193411805|gb|FK380340.1|FK380340
EST:     ATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATACTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: ATTCAATCCATTGCGACTACTTCAATGTCTCAAGAAT-CTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|20814943|gb|BQ299421.1|BQ299421
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
EST: gi|20815079|gb|BQ299557.1|BQ299557
EST:     CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCAT                         GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA
genomic: CATTCAATCCATTGCGACTACTTCAATGTCTCAAGAATCTGAGAATGCATgtaaggttta ... aattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggagttcttatctgctttgttctgttgcattttggtgaaacaaattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA
                                               ttcttc  CT-rich tract
                                        aaacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggtgaaacaaattcttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG