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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatatcattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttcatttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC

Basic information

species Glycine max
transcript GLYMA13G00950.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G086573_T01 (Zea mays), 3'ss of exon 4
gtgagtatatcattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttcatttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
                                                               || | ||||| | |   |  | | |||  || ||| |  |||  |||  | ||   |||  || ||| || |  ||||  ||  | |    |  | |||| ||  |   ||           |  |||||| ||||| ||||| || ||||| |||||||| || ||||| |||||| | |||||||||||| | |  ||||||||||||||||| 
--------------------------------------------------------------gta-agaactgattaa--acaagcttcatgtttatttc--attatcca--tgcatcatctcgtcaagc-agaagcatcacattgctgatggtactattttttttcatgaatc-----------tgaagGTGGCTATGATAAGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCAGCTTTGAAGTACTGGGGTTCTAGCACCACCACCAACTTTCCG

upper sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G57390.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtatatcattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttcatttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
                     |||  ||  || |   || | | || |  ||| |  ||  |     || || ||  ||  |  |  |  |||| ||| | | | |   |  ||   |||||  |     |   ||  |  | ||| | |  || | | ||              |||  | ||||  |||||||||||| ||||||||||| ||||| || |||||||| || |||||||| ||||| |||||||| || || || || || || || 
--------------------gtgagttc--caataaattct-ctatta--aacaatttattt-----catctctttcttctttcttgtgtatttaatt-cccttctgaaacgttatcattctctttatatttaaat--ttgtattaat-atgaagtaaatt-------------gtttgttatgtt-cagGTGGTTATGATAAGGAAGATAAAGCAGCTAGAGCTTACGACCTTGCAGCTCTTAAGTATTGGGGTCCTACAACTACGACTAATTTCCCG

upper sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0052g00840.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtatatcattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttcatttatgatcatcaatttgattgcgcatttcccagattcagattcttctctag--ctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
                                            |  |   | | ||| |   |   |   |  | | | |||||  |  | |   |||   |      |||||| |||  | ||  |    |  |||  ||||||| |      |   | |||| ||| ||  |   ||| |   ||  |||||| ||||| |||||||| |||||||| || ||||| |||||||| ||||| |||||||||||||| || |||||||| ||||| || 
-----------------------------------------gtgagta-ggatctcat-ctcgtggtcttgtcctgaatcatgatttttcact--gttgaataa----aagattctgatattccttcaagttttagattctcattttgg------atcaatttttatttatttatttattttttgtttgcagGTGGGTATGATAAGGAAGAGAAGGCAGCTAGAGCTTATGATCTCGCCGCTCTTAAGTACTGGGGTCCGACCACCACCACTAACTTCCCT

upper sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtgagtatatc-attactaccttgacctcatcattttgttttaccatcacaaaccacataca-tatatacaactgttcatttatgatcatcaatttgattgcgcatttc----ccagattcagattcttctctagctaggataatcattttag----tcaaaa---aatgacttttgtttcttcttccttttctgtgttata----gGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
   ||| |  |   | |   | |       | ||    |||  | || ||  |  |    |  | |  | | ||| ||    | |   |  | |  | ||     ||||       |||     ||||  | | | |  | | |  |      ||    |||  |   ||||  ||| |   ||    | |  |  |   ||||    || || ||||| || ||||| ||||||||||| || |||||  | ||||| ||||| ||||||||||| |  ||||||| ||||||||| 
gtatgactggagggacttgaagcacagaaccctctccatgtgcttccttctgagccgttgtgaagttcaaagaacagtctgctgaaagtt-tgagctagaacagtcattggatgatcaggcgatgattgctatgtggtgaaggttgtatacgcagcatctcacgatctaatgtgtttgggcactgtcacgtgctgcgcagTATACTTAGGAGGATATGATAAAGAAGAAAAGGCAGCCAGAGCCTACGACTTGGCAGCGCTCAAATACTGGGGTCCCAGCACCACCATCAACTTTCCG

upper sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtatatcattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttcatttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgt-tatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
                                                                                     |  || | |  ||  |    |     || |  ||| ||||| |    |||     | ||| |        ||  |||  |||||| ||   || |  | |   |||| || |||||   ||| || |||||||| || ||||||||||| |||||||||||||||||||| || || || || || |||||||| 
-----------------------------------------------------------------------------------tcctccagtgtacttaggtgagtaatctat-cgaatttttctcgattgtggagctaaacttttg-------gtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG

upper sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
---gtgagtatat-cattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttca---tttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
    ||  || |    ||   |  ||    ||||  |||| |||  |  |           | | |   |  | |||       ||| || |     | |||||    | |       | | || |   |            |  ||    | ||  |   |  ||||||| |  || ||| ||   | |    |||| || |||||   ||| || |||||||| || ||||||||||| |||||||||||||||||||| || || || || || |||||||| 
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagcta-aacttttggtggtt-ttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG

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|7795291|gb|AW780688.1|AW780688
EST:     GGAAAGGAAGACAAGTTTACCTGG                         GTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCT
genomic: GGAAAGGAAGACAAGTTTACCTGG
EST: gi|37995737|gb|CF807326.1|CF807326
EST:     GGAAAGGAAGACAAGTTTACCTGG                         GTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCT
genomic: GGAAAGGAAGACAAGTTTACCTGG
EST: gi|17021856|gb|BM092890.1|BM092890
EST:     AGTTTACCTGG                         GTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCT
genomic: AGTTTACCTGG
EST: gi|6481417|gb|AW200688.1|AW200688
EST:     GGAAAGGAAGACAAGTTTACCTGG                         GTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCT
genomic: GGAAAGGAAGACAAGTTTACCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC
                       cttttgtttcttcttc  CT-rich tract
     attttagtcaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatatcattactaccttgacctcatcattttgttttaccatcacaaaccacatacatatatacaactgttcatttatgatcatcaatttgattgcgcatttcccagattcagattcttctctagctaggataatcattttagtcaaaaaatgacttttgtttcttcttccttttctgtgttatagGTGGTTATGACAAGGAAGATAAGGCAGCCAGGGCTTACGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACCAACTTTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC