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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

Basic information

species Glycine max
transcript GLYMA04G09070.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatataca-tattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
              ||     ||||     | |      | |||||       |||| |  | | ||   | |  |||||   ||   | |     |  || | ||| ||    | | | ||| || |  ||   |||||||||||| ||||| |||||||| ||||| || || ||||| |||||||| ||||  || || || |||||||||||  ||||
-------------gagaagccattcacagcgcaa---acacttgggtgtcttgtaatgtttactgttggtatttattatgagcaagaagccaag--aactg-acttgaatg---cttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGC

upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
           | ||| |   |||          | |    | | ||  |  | | | ||     ||  ||| ||       | ||   ||    | | | |||    |||  |  |  ||| || || ||    |||||||| || ||||| || || || || || || |||||||| |||||||||||||  || || |||||||| |||||||||||
----------gtcaagctgcgatt----gcaagcttttagctggaggctgtgacagtttatggtattgcacttgt-------agatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC

upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
            | |   |    |  |||      | | ||    |  ||     || ||  | |    ||| |   |   ||||     |  | |||    |||    || ||  |  ||| || || ||    ||||| ||||| ||||| |||||| | ||||| || || ||||| |||||||| ||||  || || || |||||||||||||||||
------------ggaaaatgagctactcaatccccgggaatcccagaggg----gatttaagtttccaaactagccctaaataaacaag-taatgactctggtttt--ctgttc--tccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC

upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
                       | ||| ||| ||     ||| |  ||    |   | |  |||||    |  |||| | |   |     | ||  |   ||||| |||         ||| |||||||| ||||| |||||||| |||||||||||||| ||||| || |||||||| || ||||| ||||| ||||| |||||||| ||  | |||||
----------------------gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgtt--ttatctctgtttcacagttttcatc--atttgtatt--------cagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC

upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
                          | | || |    |||||||        | ||  |  |  | ||||    | | | || |||   | |||   |  ||||  |||||  |    |||||| || ||||| || || || || ||||| |||||||| ||||| || |||||||| || ||||||||||| || || || ||||||||  |||||||
-------------------------gtta-gtctaacatatttggc-------tgatggat-ttctatgacaaaatttatctatatt--ttgcttgacttcatttc-attgactcc---agGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCAAGTGGATAAATAAAAAATGGAGGGAGGGTTTCTATGTCACCTCTATGGC

upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
gttaatacccctgaagtttttattcttcat-gtattgtgtatttggggtggcaataatatacata-ttttgactggttatgtttaaattgtcttctta-cttgtatttggattg-atccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
                        | |||| ||  | | || ||   ||     |   ||   || |||||| |  ||  || | |||  || |  || ||  | |   ||||   |  |   ||| ||    ||   |||||| || || ||||| ||||| || |||||||||||||||||||| || |||||| ||||||| || || || ||  |||||||
------------------------cgtcatagtcctttttaattttagttattttttaatttttagttttgagttatt-cgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC

upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
                                                 ||| || | |  |    ||| ||  || || | || |   ||     | | |    | |   |  |||    | |  ||||| | ||||    | |  | |    |  || ||   | |||| ||   ||||   ||||| || || ||||| || || || |||||||||||||||||||| || |||||| ||||||| ||||| || ||| | |||||
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgat-ctcaagggtgtttgatgatttat-tcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
                                                     || | |   | || |   |||  |   |   ||||||  || ||  || |||        ||    ||| || |  |||   || ||||| || ||||| || ||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| || ||| | |||||
----------------------------------------------------gtattgtcgctgttattgatggcca--ctggcattgtcg-ctgacgcgtgttt-------cccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgttta--aattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
                                                              |||| |  ||| |  || |    | | |  || || ||      ||  |    ||    ||| || |  |||   || ||||| || ||||| || ||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| || ||| | |||||
-------------------------------------------------------------gtattgtcgctgttattgatggccactggcattgttgctgacgcgtgattc---ccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

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|193616008|gb|FK569670.1|FK569670
EST:     GCCGGGGCTAATAATGGATCCTCATTGGTTGTAATGTCTAAAG                         GTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTA
genomic: GCCGGGGCTAATAATGGATCCTCATTGGTTGTAATGTCTAAAGgttaataccc ... atccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
                                              tcctttt  CT-rich tract
        ttatgtttaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA