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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggtcccctttatccttgggacgcattgtggtttttctttgtgctagccctagaccccggtatatatcacaaagcgtatatttcaagcatggagcttattttatttttctctggcagggaatttttggaaaataaaacaataatatttttgtcgaaatctaatcactgcttcatgtattggatattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATACCAACTAGAGGATTTAGAGGTTGTCACCGCAGACTACATGTTGAAAGTGG

Basic information

species Glycine max
transcript GLYMA11G12610.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12610.1 (Glycine max), 3'ss of exon 16
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 15
gtactggtcccctttatccttgggacgcattgtggtttttctttgtgctagccctagaccccggtatatatcacaaagcgtatatttcaagcatggagcttattttattt----ttctctggcagggaatttttggaaaataaaacaataatatttttgtcgaaatctaatcactgcttc-atgtattggatattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATACCAACTAGAGGATTTAGAGGTTGTCACCGCAGACTACATGTTGAAAGTGG
||||  ||    |      ||      |||  |  | |||  ||   ||     | ||||||   |||  |     ||    | ||  || ||  || || ||||         | |     |     |  ||    | | |||||||  | |  | | |    |  |  |   |||||  ||| ||  | ||   | ||||||||||||| ||| |||||  ||||||||||||| || |||||||| ||||| ||||||||| | ||||||||  | | ||| |||||| |||||||||
gtacatgttaaataggctattcacttccatctttttatttacttacactgaaaat-gaccccataatactttgtggagaac-tcttataaacaacga-ctcatttggagaggagtaccagaacgactcaaattaatcacagaaaacaaagaaaactctctaactacattgtttgtgcttttatgaatgtgtta--aaacagGTTGACCCAAGCACAGGTGAAGCAGAAGATGATGGAGTAGAAGATGAGTACCAGCTAGAGGATCTTGAGGTTGTAGCTGGAGATTACATGGTGAAAGTGG

upper sequence: GLYMA11G12610.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 16
gtactggtcccctttatccttgggacgcattgtggtttttctttgtgctagccctagaccccggtatatatcacaaagcgtatatttcaagcatggagcttattttatttttctctggcagggaatttttggaaaataaaacaataatatttttgtcgaaatctaatcactgcttcatgtattggatattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATACCAACTAGAGGATTTAGAGGTTGTCACCGCAGACTACATGTTGAAAGTGG
                                                                                       |||  |   |    | |  |   | ||     |  ||     |  ||  |  ||||| ||   || |       | | |||| ||  |  ||| |   |||||  ||||||||| ||||| |||||||||||||| || ||||| || ||||| |||||||| || |||||  | || |||||  | || || ||  ||||||| || |
---------------------------------------------------------------------------------------caaatagaaattacactagaggatgcttccatactgatgaact--aatctccaacaaaaaa--ttctacatggttttcatca-tgtgttttgttt---atattt-ccagGTTGATCCAACTACTGGTGAGACAGAGGAAGATGGTGTCGAAGACGAATACCAGCTGGAGGACCTTGAAGTTGTTGCAGCTGATTATGTGTTGAAGGTTG
















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|192314535|gb|FK006349.1|FK006349
EST:     TGTCAATTGCTGGAAAATTTTCTAACGTTCTGAAATTTATTGTTAAAGAG                         GTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATAC
genomic: TGTCAATTGCTGGAAAATTTTCTAACGTTCTGAAATTTATTGTTAAAGAGgtactggtcc ... tattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATAC
EST: gi|58018608|gb|CX705350.1|CX705350
EST:     TGTCAATTGCTGGAAAATTTTCTAACGTTTTGAAATTTATTGTTAAAGAG                         GTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATAC
genomic: TGTCAATTGCTGGAAAATTTTCTAACGTTCTGAAATTTATTGTTAAAGAGgtactggtcc ... tattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATAC
EST: gi|192324349|gb|FK018325.1|FK018325
EST:     TGTCAATTGCTGGAAAATTTTCTAACGTTCTGAAATTTATTGTTAAAGAG                         GTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATAC
genomic: TGTCAATTGCTGGAAAATTTTCTAACGTTCTGAAATTTATTGTTAAAGAGgtactggtcc ... tattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATAC
EST: gi|192314534|gb|FK006348.1|FK006348
EST:     TGTCAATTGCTGGAAAATTTTCTAACGTTCTGAAATTTATTGTTAAAGAG                         GTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATAC
genomic: TGTCAATTGCTGGAAAATTTTCTAACGTTCTGAAATTTATTGTTAAAGAGgtactggtcc ... tattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataatatttttgtcgaaatctaatcactgcttcatgtattggatattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATACCAACTAGAGGATTTAGAGGTTGTCACCGCAGACTACATGTTGAAAGTGG
                   atctaat  putative branch site (score: 3)
     atatttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactggtcccctttatccttgggacgcattgtggtttttctttgtgctagccctagaccccggtatatatcacaaagcgtatatttcaagcatggagcttattttatttttctctggcagggaatttttggaaaataaaacaataatatttttgtcgaaatctaatcactgcttcatgtattggatattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGCGTTGAAGATGAATACCAACTAGAGGATTTAGAGGTTGTCACCGCAGACTACATGTTGAAAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT