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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaattcaaggataatgtatgcaacaacaatctctgctttcttgcatattgaacaagaagtttatataaatgaattaattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG

Basic information

species Glycine max
transcript GLYMA08G03630.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G03630.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 2
gtaagta--attcaag--gataatgtatgcaacaacaatctctgctttcttgcatattgaacaagaagt--ttatataaatgaattaattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
||||||    || ||    ||  ||| |   | | ||  |   |  ||     | | | |||  | ||   ||   | ||| ||||   | ||      | ||||| ||| || || || ||  | || || ||  |||||||    || || ||||||||||||||||||||||||||||||||| |  ||||  ||
gtaagtcttgttgaaatcaattgtgtgtttgaaagcatgcagagtattacaata-agtaaacttgcagccattggttgaatcaattgtgtgtttgggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTG

upper sequence: GLYMA08G03630.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143817_T01 (Zea mays), 3'ss of exon 3
gtaagtaattcaaggataatgtatgcaacaacaatc---tctgctttcttgcatattgaacaagaagtttatataaatgaattaattcttaaattct-----acagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
    |||| | || | |  | |   || | |  ||    | || || ||| || | |  | |  || |||| || |         || | |||||       | |||| |||||||||||||    | || || ||| ||||||||  ||||||||| |||||||||||||||||||||||||||||| |  ||||||||
----gtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatat-aattttaaatcaggttggggtttttgaaatttctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG

upper sequence: GLYMA08G03630.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G117388_T01 (Zea mays), 3'ss of exon 3
-------------------gtaagtaattcaaggataatgtatgcaacaacaatctctgctttcttgcatattgaacaagaagtttatataaatgaattaat-tcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
                      | | |||  |  ||| ||    ||   |  | || |   |  ||| | ||| | |      | | |  |  ||  |||   | ||      | ||||| |||||||||||||    | || || ||  ||||||||   |||||||| |||||||| ||||||||||||||||||||| |  ||||||||
gtaggttaaagttttgctgactactgattataaaatagtg---acagttatgaactatctataattgtaaatt-agctttggttgtttggatttgctttatcgtgttttggcatgcagAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTG

upper sequence: GLYMA08G03630.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G29330.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtaattcaaggataatgtatgcaacaacaatctctgctttcttgcatattgaacaagaagtttatataaatgaattaattctta-aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
|| || | | | |   | |  |||  |   |  | |   |||   ||  || || |         |||| | ||   | |  ||   |  ||| | ||||| ||| ||||| || ||||| |||||||| ||||||||  | ||||| || || || |||||||||||||| |||||  ||||  | ||||||
gtgagca-tactattttcacatatatag--atgaacaaagctaatttcgattttta---------ttatcttaacatactcttttaaatgattgtgcagAGCAAGATATGGAGTTCAACTCGAGAAAGGGCCATTTGAAAGGCGGACAGCAGACTTTTTGTGGATGATGATCTTTGGATCCTTCACTCTATTG

upper sequence: GLYMA08G03630.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g00510.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------gtaagtaattcaaggataatgtatgcaacaacaatctctgctttcttgcatattgaacaagaagtttatataaatgaattaattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
                                                                                |||| |  |  |  | |  |    | | |   ||    ||||| | || |   |          |  || || ||     ||   |  | |  |||||||  || ||||| ||||| || ||||| |||  ||||||  | || || || |||||||||||||||||||||||||| ||  |  || |  ||
gtaagtgtaactgtgtaaatcccagaagcttctcttgagttcaccctgaagtctgtgtgcacacttttgtggatttccatgtaacttgtctagagtttgtaggggaaccttgaaaaattgctt-catggaacctacctttaccctgcatttacatactgcaaagttatattgttacagAGCCAGATATGGGGTCCAGCTGGAGAAGGGAGTATTTGAAAGGCGCACGGCAGATTTCTTGTGGATGATGATATTTGGAGCTCTGACATTGCTG

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|192308725|gb|FG999764.1|FG999764
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|213599245|gb|DB960013.1|DB960013
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|151406483|gb|EV276298.1|EV276298
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|4305349|gb|AI443749.1|AI443749
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|192332520|gb|FK025625.1|FK025625
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|42723245|gb|CK769144.1|CK769144
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|8827592|gb|BE211322.1|BE211322
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|19452471|gb|BM953881.1|BM953881
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|298172446|gb|HO019486.1|HO019486
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|298183475|gb|HO028688.1|HO028688
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|22524785|gb|BU083596.1|BU083596
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|298169339|gb|HO020699.1|HO020699
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|21887095|gb|BQ740308.1|BQ740308
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|192332519|gb|FK025624.1|FK025624
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|298171588|gb|HO021180.1|HO021180
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|193672594|gb|FK615912.1|FK615912
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|192308360|gb|FK001346.1|FK001346
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
EST: gi|22522837|gb|BU081648.1|BU081648
EST:     TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT                         AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC
genomic: TTTTTCCTTGGACCATTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgcatattgaacaagaagtttatataaatgaattaattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
                                 aattaat  putative branch site (score: 3)
            aacaagaagtttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaattcaaggataatgtatgcaacaacaatctctgctttcttgcatattgaacaagaagtttatataaatgaattaattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGATCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT