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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatccatggtcaagcttcaaaagattaatatttgcagtgcatcaaggaaaaattataggagaaacaattatgattttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT

Basic information

species Glycine max
transcript GLYMA19G13070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G168752_T01 (Zea mays), 3'ss of exon 4
-------------------------aaaatccatggtcaagcttcaaaagattaatatttgcagtg------catcaaggaaaaattataggagaaac---aattatgattttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
                           | |  |||  |   ||  || |    | |||    |||        ||||    |||  | |     |  |   ||      |  |||| ||| || ||   ||||||||||  ||   || |||||||||||  ||||||| ||||| ||||| || || || |||||||||||||||||||| || |||||||| ||||||||||
gttggctaccaatcttgagcggaacttagttgatgagctcactataacaaccaactatgcttagtttacatttatcagatgaaagatgtcatttatcctctaagctctttcatgcttactcatttatcattcagGGCATACTAAGGCTGCGTGGTAGACCTTCTGTTGCATATGATCAACAGGGACTTGTTTTTGCTGTAGCAATGGAAGGTGGTGCTATTAATTTATTTGATT

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G079723_T01 (Zea mays), 3'ss of exon 4
---------------------aaaatccatggtcaagct---tcaaaagattaa---tatttgcagtgcatcaa--ggaaaaattataggagaaacaattatgatttt-----gctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
                     ||| |   | |   ||||   |  |   |  ||   |  ||    | |||  |  |||  ||  ||   |   |   |   |  | |     ||| ||| || ||    |||||||||  ||   || |||||||||||  |||| || ||||| || || || || || |||||||||||||||||||| || |||||||| ||||||||||
gttggctaccaattttgagtgaaacttagttgatgagctcactatagcaaccaactatgcttattttacatttatgggatgaaagatgctatttatcctcgaggctctttcatgcttactcatctatcaatcagGGCATACTAAGGCTGCGTGGTAGACCTTCTGTCGCATATGATCAGCAGGGACTTGTTTTTGCTGTAGCAATGGAAGGAGGTGCTATTAAGTTATTTGATT

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G079723_T02 (Zea mays), 3'ss of exon 3
----aaaatccatggtcaagcttcaaaagattaatatttgcagtgcatcaaggaaaaattataggagaaacaattatgattttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
      | |  |    | | ||        || | ||||   |      |      | ||||    ||  |  ||    |  |||| ||| || ||    |||||||||  ||   || |||||||||||  |||| || ||||| || || || || || |||||||||||||||||||| || |||||||| ||||||||||
gagctcactatagcaaccaactatgcttattttacatttatgggatgaaagatgctatttatcctcgaggctctt----tcatgcttactcatctatcaatcagGGCATACTAAGGCTGCGTGGTAGACCTTCTGTCGCATATGATCAGCAGGGACTTGTTTTTGCTGTAGCAATGGAAGGAGGTGCTATTAAGTTATTTGATT

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G14530.1 (Arabidopsis thaliana), 3'ss of exon 5
------aaaatccatggtcaagcttcaaaagattaatatttgcagtgcatcaaggaaaaattataggagaaacaattatgattt-tgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
      |  |  ||| |  ||  || |     || |  ||   | |   ||   |||   ||||| |        | ||||| | |||| ||   | ||||    |||| ||  ||||||||||||||||||| || ||||||||||||||||||||||| || |||||  | ||||||||||| || ||| |||||||||||||||
ggaaccacgaaacattgagaatatttaggctctttaccttaatactctctctgtgaa--tttatatggt-----ttcatgatctatgcttacccttttagtcaatagGGAATTCTACATCTACGTGGTAGACCTGCAGTTGCGTATGACCAACAAGGCCTTGTGTTTGCAATTGCAATGGAAGGAGGTGCTGTTAAATTATTTGATT

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0066g00720.t01 (Vitis vinifera), 3'ss of exon 5
-----aaaatccatggtcaagcttcaaaagattaatattt-gcagtgc-atcaaggaaaaattataggagaaacaattatgattttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
      |  |   | ||  |   |  ||    |   |||| | | | | |||  || ||||||| | ||       || ||||| |||| |||| |||||||||||||| || |||| |||||||||| ||||  |||| || ||||||||||| ||||| |||||||| || |||||||||||||| ||||||||||| |||||||
atttggagttgggtagtttaatattgaagtcatgccattttgtactcctatccggggaaaattacatga-------ttgtgattgtgcttactgttatagttttcagGGGATTTTACGTCTACGTGGTCGACCTACTGTCGCATATGACCAACAGGGCCTTGTCTTTGCGGTGGCAATGGAAGGGGGTGCTATTAAATTGTTTGATT

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S27_191V6.1 (Physcomitrella patens), 3'ss of exon 5
aaaatccatggtcaagcttcaaaagattaatatttgcagtgcatcaaggaaaa--attataggagaaacaattatg-attttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
    |   ||        | |        || ||      || | ||   ||   ||  | |   |  |  || ||     || || |     |  | || ||||  | || | | |  | ||||||||||||||||||||||| ||||| ||||| || ||| ||||||| ||||||   |||||||| ||| |||||||  
---gtttttgaatggagctgaggcttccgattttaatgtcgcttaaacccaagttatcttcgtccagtcgtttttgtgcactgatcgcaatactgctgtttagGGACTTTTGCGTGTGAGGGGTAGACCCGCTGTTGCGTATGATCAACAGGGCCTTGTATTTTCTGTAGCTATGGAAAATGGAGCTATCAAACTATTTGACG

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S109_268V6.1 (Physcomitrella patens), 3'ss of exon 5
-aaaatccatggtcaagcttcaaaagattaatatttgcagtgcatcaaggaaaaattataggagaaacaattatgattttgctcac-tgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
            | ||  |||| ||| ||     | |     ||||| | |     | |    |||     | | |   |  | || ||||      | |||||  | || | | |  | ||||||||||||||||||||||| || || || || || |||||||| || |||||||| |||||||||||  | |||||  
ggccgagaggaataaatattcataagctt--ctgtagagtctcatcatgtatccccttttcttgaagtgtcttttacgctaatgacatgattgctgctccagGGACTATTGCGTGTGAGGGGTAGACCCGCTGTTGCGTATGATCAGCAGGGTCTTGTATTTGCTGTGGCTATGGAAGGTGGAGCTATTAAGCTCTTTGACG

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ21865 (Selaginella moellendorffii), 3'ss of exon 4
aaaatccatggtcaagcttcaaaagattaatatttgcagtgcatcaaggaaaaattataggagaaacaattatgattttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
                      ||||  ||   ||    ||| |          || |   ||||     | ||  |  |  || |   ||  |||   || | ||||| |  | || || ||||   |||| |||||||| |||||||||||||| |||||||| || |||||||| ||||| || ||  | |||||  
--------------------gtaagaaaaactcttttcttgcgtt---------ttcttccagaa----ctttggcta-gagcatttccatgatttcagGGTCTTCTTAGAG-TCCGGGGAAGACTGTCTGTGGCGTATGATCAACAAGGCCTGGTATTTGCTGTTGCCATGGAAGGCGGAGCAATCAAGCTGTTTGACG

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ21867 (Selaginella moellendorffii), 3'ss of exon 5
aaaatccatggtcaagcttcaaaagattaatatttgcagtgcatcaaggaaaaattataggagaaacaattatgattttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
                      ||||  ||   || |  ||| |          || |   ||||     | ||  |  |  || |   ||  |||   || | ||||| |  | || || |||||  |||| |||||||| |||||||||||||| |||||||| || |||||||| ||||| || ||  | |||||  
--------------------gtaagaaaaactctttccttgcgtt---------ttcttccagaa----ctttggcta-gagcatttccatgatttcagGGTCTTCTTAGAG-TCCGGGGAAGACCGTCTGTGGCGTATGATCAACAAGGCCTGGTATTTGCTGTTGCCATGGAAGGCGGAGCAATCAAGCTGTTTGACG

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|192321958|gb|FK012510.1|FK012510
EST:     CTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG                         GGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGC
genomic: CTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAGgttggtagtt ... tagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGC
EST: gi|58015238|gb|CX701980.1|CX701980
EST:     CTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG                         GGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGC
genomic: CTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAGgttggtagtt ... tagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGC
EST: gi|58016158|gb|CX702900.1|CX702900
EST:     CTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG                         GGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGC
genomic: CTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAGgttggtagtt ... tagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggaaaaattataggagaaacaattatgattttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT
                                                ttttc  CT-rich tract
                  aaacaattatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatccatggtcaagcttcaaaagattaatatttgcagtgcatcaaggaaaaattataggagaaacaattatgattttgctcactgatatagttttcagGGCATCTTACATCTACGTGGTAGACCCGCTGTTGCGTATGACCAACAAGGCCTGGTCTTTGCTGTAGCAATGGAAGGGGGAGCTATTAAATTATTTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - catggtc
- - - - - - - agcttca
- - - - - - - - - - - - - - - - - tgcagtg
- - - - - - - - - - - - - - - - - - - - - - - - gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaaac