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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgagctttgtttcatttacatcttataacttgatatataaaaggtcctggtacctgataataaaacctgtatgacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT

Basic information

species Glycine max
transcript GLYMA19G27380.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g10810.1 (Oryza sativa), 3'ss of exon 3
---gtttgagctttgtttcatttacatcttataacttgatatataaaaggtc--ctggtacctgataataaaacctgtatgacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT
   | |||   |||| |    | | |  | ||| ||||  | |||     ||   |  |||||    | |  |    |||    ||| |||| | |      |||| ||||||||||||||||| || ||||||||||||||||| |  ||||| ||||||||  | ||    || |||   ||||| | ||||    | ||  |
tctggttgttttttggtatcataagaaat-atatcttgccaaataccttctctatttctacctttagacattattattatttt-taataatgatatact---cagATACAATGATGAAGTTTGCATCCTTTGAGACCATTGTTGAACAAATCTACAAGCATGCTGTTCCTGTCCCGAAGTCAGAGTGTAGCAAATCATTCCAGTT

upper sequence: GLYMA19G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
gtttgagctttgtttcatttacatcttataacttgatatata-aaaggtcctggtacctgataataaaacctgtatgac-ataaaaatgttctttcttg--cagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT
      || | |   || | |  | || |   || || | ||  |  |   || |  |   | ||     || |    | ||  ||   |||  || ||  |||| || |||||||||||||| || |||||||||||||||||  ||||||| ||||| ||  | ||    || |||  |||||||| |||     | ||| |
----tggcatggcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT

upper sequence: GLYMA19G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g37600.1 (Oryza sativa), 3'ss of exon 3
gtttgagctttg---tttcatttacatcttataacttgatatataaa-aggtcctggtacctgataataaaacctgtatgacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT
    ||||  ||   ||   | | || |    |  ||| |||        | | ||    ||  | || |||  |   | |  | |  || || |      |||| || |||||||||||||| |||||||| ||| |||||||| |||| || ||  |||| |||||  | || |||| |||||||| ||||   ||||| ||
----gagcactgatattcagtatgcagcaatcagattgttatcccgttgagccttgagtgcttttcatgaaatttaattaatttgaccattttatgatacacagATACTATGATGAAGTTTGCGTCTTTTGAAACCGTTGTTGAGATGATATACAAATATGCAATCCCTGCCCCCAAGAGTGAGTGCAGCAAACCACTGCAGCT

upper sequence: GLYMA19G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G152827_T01 (Zea mays), 3'ss of exon 3
-gtttgagctttgtttcatttacatcttataacttgatatataaaaggtcctggtacctgataa-taaaacctgtatgacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT
  ||||    |||| | || ||  | ||||   ||    |  ||    |  |   |  | ||||    |||        |       | |  | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||||||  | ||    || |||  |||||||| ||| |     ||  |
aatttggtagttgtattatatat-ttttatctattctcgttcaagccatattctcatattataagctgaactcacccatcgcccttgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: GLYMA19G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G015401_T01 (Zea mays), 3'ss of exon 3
-gtttgagctttgtttcatttacatcttataacttgatatataaaaggtcctggtacctgataa-taaaacctgtatgacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT
  ||||    |||| | || ||  | ||||   ||  | |  ||    |  |   |  | ||||     ||        |       | |  | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||||||  | ||    || |||  |||||||| ||| |     ||  |
catttggtagttgtattatatat-ttttatctattcttgttcaagccatattctcatattataagctgtactcacccatcgcccttgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: GLYMA19G27380.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G060630_T01 (Zea mays), 3'ss of exon 3
--gtttgagctttgtttcatttacatcttataacttgatatataaaaggtcctggtacctgataa-taaaacctgtatgacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT
   ||||   ||||| | ||  | |  ||||   ||   ||  ||    |  |  ||  | ||||     ||     ||    |    | |  | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| || || ||||| ||  | ||    || |||  |||||||| ||| |     ||  |
taatttggtatttgtattat--ataatttatttattatcatgcaagccatattcttatgttataagctgtactcacctgttgcactcgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATATACAAGCACGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

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|207681920|gb|GD662037.1|GD662037
EST:     GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCAT                         ACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGAT
genomic: GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCATgtaagttgac ... tttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGAT
EST: gi|10845648|gb|BF068722.1|BF068722
EST:     GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCAT                         ACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
genomic: GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCATgtaagttgac ... tttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
EST: gi|207703091|gb|GD684883.1|GD684883
EST:     GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCAT                         ACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
genomic: GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCATgtaagttgac ... tttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
EST: gi|298168584|gb|HO009514.1|HO009514
EST:     GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCAT                         ACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
genomic: GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCATgtaagttgac ... tttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
EST: gi|192295707|gb|FG990561.1|FG990561
EST:     GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCAT                         ACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
genomic: GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCATgtaagttgac ... tttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
EST: gi|58024028|gb|CX710769.1|CX710769
EST:     GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCAT                         ACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
genomic: GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCATgtaagttgac ... tttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
EST: gi|208231650|gb|GE034441.1|GE034441
EST:     GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCAT                         ACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA
genomic: GCTGTACAAGGGGTTAGTGCCTCTCTGGGGACGACAAATTCCATgtaagttgac ... tttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcctggtacctgataataaaacctgtatgacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT
         acctgat  putative branch site (score: 4)
                                        tgttctttctt  putative PPT
                                 ataaaaatgttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgagctttgtttcatttacatcttataacttgatatataaaaggtcctggtacctgataataaaacctgtatgacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -ctggtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa