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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaatcaaattctgtttcggattatgcacttttatagatagatgacatgcataattctattttatcactctaaaaactgaatacattcttttgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA

Basic information

species Glycine max
transcript GLYMA04G42830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g43570.1 (Oryza sativa), 3'ss of exon 4
-----gta-tccaatcaaattctgtttcggattatgcacttttatagatag-atgacatgcataattctattttatcactctaaaaactgaatacattcttttgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA
     ||  |   |  |||     ||    ||| || | || || |  ||    |  | |  ||| | ||| | |    | |  | ||     | ||||           || ||||| |||||||| ||||||||||| || |||||||| ||||| ||  |  | ||||| ||||| || |||||   |||||| |||||
tctctgtgctattagtaaacagctttcttcattttgta-ttatacaattattgggttaggggtaagtttatctaacttttttcgatacatggaaaattc-----------agATTTGGACCATACTTCTGCCAGCCTGTTATCGCTGGACTTGGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G045371_T02 (Zea mays), 3'ss of exon 3
gtatccaatcaaattctgtttcggattatgcacttttatagatagatgacatgcataattctattttatcactctaaaaactgaatacat-tcttttgca--tttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA
      |||  |    |  |||  ||||    |||||||    | || ||  | |    |  |||  |    |     ||||     |||  |   || |  |||||| ||||| ||||| || |||||||| || ||||||||||| ||||||||  ||  |||||||||||| || |||||   | | || |||||
----ttaattcatagttacttcaaatta---gcttttatgttcaaat-actggtactgattaattgcaatgtttgtctaacttttatcatgccacatgaaactttcagATTTGGGCCATATTTCTGCCAGCCAGTCATTGCTGGACTTGGAGATGACAACGTACCATTCATTTGTACCATGGACTGCCTCGGTGCAAA

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G092975_T01 (Zea mays), 3'ss of exon 3
gtatccaatcaaattctgtttcggattatgcacttttatagatagatgac-atgcataattctattttatcactctaaaaactgaatacattcttttgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA
      ||||      || | |  ||||    |||||||    | ||    |  | |   |      | |   | |||    |      |  | |     |||||| || || ||||| ||||||||||| || ||||||||||| ||||||||  ||  |||||| ||||| || |||||   | | || |||||
---cttaatccgtagttgctgcaaatta---gcttttatcttcaaatactgaaactttcattggcaatgtttgtttaacttttatcatgacacatgaaactttcagATTCGGGCCATATTTTTGCCAGCCAGTCATTGCTGGACTTGGAGATGACAACGTACCATTTATTTGTACTATGGACTGCTTAGGTGCAAA

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 3
------------gtatccaatcaaattctgtt-tcggattatgcacttttatagatagatgacatgcataattctattttatcactctaaaaactgaatacattcttttgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA
               ||   ||  | | |||| |  | || |    |  | |  | |       | | ||    || | |  || |   |  ||| | |||    || |  ||||||| ||||| |||| ||| ||||| ||||| ||||||||| | ||||||||| ||||||| ||||||||||| |||||| | |||||||| ||
gttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatgattaatgtggcattgccactactaagtaccaaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------gtatccaatca-aattctgtttcggattatgcactt--ttatagatag--atgacatgcataatt-----ctattttatcactctaaaaactgaatacattcttt--tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA
                                             | |  | |    || ||| ||| || | |    ||  || | | |||  ||||  ||| || ||     ||   | || | |   |||  | |  | |||  ||  |  ||||||| |||||||| ||||| ||||| ||||| ||||||||  | |||||||||||||| || ||||||||||| |||||  | || ||||| ||
gtcagtgtgcttgtgttgtttacttatgtagctgtattagttacctgttgatttgcgatgctgcttctgactctagttttaattctggttaggaatgatttgcttagtttgtctctgaatcatgatttagaaagataatcagattggttgctttatttcagATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 3
gtatccaatcaaattctgtttcggattat--gcacttttatagatagatgacatgcataattctatttta--tcactctaaaaactgaatacattcttttgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA
       ||||   ||    ||   ||||  ||||| || |   | | || | || || |||  | |  |  | |     |   ||||||| | | ||||   ||| ||||||||||||||||| ||||||||||| ||||||||| | |||||||| ||||| ||||||||||||||||||||| | |||||||| ||
------catcattgtcaccctccctttataagcactgttttct-ttggtgtc-tgtatgatttcaatgaagatgatatgcatttctgaatataatgtttt-ttttttagGTTTGGTCCATACTTCTGCCAGCCTGTGATTGCTGGATTGGGAGATGAAGACAAGCCATTCATTTGCACAATGGATTCAATTGGAGCCAA

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|16343834|gb|BI969429.1|BI969429
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|16996875|gb|BM086247.1|BM086247
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|298166167|gb|HO009138.1|HO009138
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|298176811|gb|HO023284.1|HO023284
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGCAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|16348632|gb|BI974227.1|BI974227
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|8401459|gb|BE057093.1|BE057093
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|192322314|gb|FK014555.1|FK014555
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|192325513|gb|FK018424.1|FK018424
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|151409085|gb|EV278893.1|EV278893
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|7588098|gb|AW703901.1|AW703901
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|8283379|gb|BE020940.1|BE020940
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|298178421|gb|HO024156.1|HO024156
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|298189628|gb|HO038031.1|HO038031
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|213605503|gb|DB968761.1|DB968761
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|6567370|gb|AW234981.1|AW234981
EST:     CCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: CCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|151397166|gb|EV267039.1|EV267039
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|151411912|gb|EV281723.1|EV281723
EST:     AAGCCCCAAACCTTTGCCGGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
EST: gi|16343936|gb|BI969531.1|BI969531
EST:     AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAG                         GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA
genomic: AAGCCCCAAACCTTTGCCAGCCTAGTCTCCGCTATTCTCTACGAGAAAAGgtatccaatc ... tgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcataattctattttatcactctaaaaactgaatacattcttttgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA
                     ctctaaa  putative branch site (score: 3)
                                       ttcttttgcatttc  putative PPT
     taattctattttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccaatcaaattctgtttcggattatgcacttttatagatagatgacatgcataattctattttatcactctaaaaactgaatacattcttttgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA