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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatttcgccctttttattttttctctccgcgtgaaaaatttgacgctatttttcgtttattctcatccgtatttttctgaaaaatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT

Basic information

species Glycine max
transcript GLYMA16G22060.1
intron # 3
splice site 3'
intron type U2

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|192307926|gb|FG998943.1|FG998943
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|10843286|gb|BF066593.1|BF066593
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|192297534|gb|FG989540.1|FG989540
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|5058411|gb|AI736943.1|AI736943
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|208284395|gb|GE086371.1|GE086371
EST:     AGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: AGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|208223726|gb|GE027057.1|GE027057
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTGTCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|192307927|gb|FG998944.1|FG998944
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|208088787|gb|GD891201.1|GD891201
EST:     AGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATAGGAAAATCGCTATCTGATGCT
genomic: AGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAAT-GG-AAATCGCTATCTGATGCT
EST: gi|193456025|gb|FK417073.1|FK417073
EST:     AGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: AGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|207692643|gb|GD674868.1|GD674868
EST:     AGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: AGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|192298517|gb|FG989208.1|FG989208
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|208080846|gb|GD876656.1|GD876656
EST:     AGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAAATGGAAATCGCTATCTGATGCT
genomic: AGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTG-AAAAATGGAAATCGCTATCTGATGCT
EST: gi|192325043|gb|FK015449.1|FK015449
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|208079717|gb|GD875401.1|GD875401
EST:     CAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: CAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
EST: gi|17401598|gb|BM178380.1|BM178380
EST:     TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTT                         GTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
genomic: TCAGAGAGCAGTTCAAGAAGGAGCATCCTAACAACAAATCCGTCGCTGTTgtgagtgatt ... aatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgacgctatttttcgtttattctcatccgtatttttctgaaaaatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT
 atttgac  putative branch site (score: 4)
                                tatttttctgaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgatttcgccctttttattttttctctccgcgtgaaaaatttgacgctatttttcgtttattctcatccgtatttttctgaaaaatattttagGTCGGCAAAGCTGGTGGTGAAAAATGGAAATCGCTATCTGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG