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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtaaacattaataattggtttgtacttccttctatgcttacctaattcttgggaactcgttttacaaactttttactaatctagagaccaatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAATGTTGTAACCATCCCTACCTCTTTGTGGGTGACTATGATATCCATAAACA

Basic information

species Glycine max
transcript GLYMA11G00640.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G00640.2 (Glycine max), 3'ss of exon 10
lower sequence: AT5G19310.1 (Arabidopsis thaliana), 3'ss of exon 10
ctgtaaacattaataattggtttgtacttccttcta---tgcttacctaattc--ttgggaactcgttttacaaacttt--ttactaatctagagaccaatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAATGTTGTAACCATCCCTACCTCTTTGTGGGTG---ACTATGATATCCATAAACA
  ||    |   | | |||   |    |||  || |   ||||| | |  |||  |   ||||     | |  || ||   || |||||  ||   |  || || |||   ||| |||||||| ||||| |||||  ||||||||||| | ||||| |||||||||||||| ||||| || || || |   | ||| | ||   |||   
--gtttgtagctaaacttgaacttccattctctccaaaatgctttcatctttcggtaaagaacataagtcaggaagttaaattgctaatggagtc-cttatgtgcagGCAATGGGAAATCAAAGAGTCTGCAGAATCTGACAATGCAATTAAGAAAGTGTTGTAACCATCCGTACCTATTCGTTGGAGCAGATTATAACATGTGTAA---

upper sequence: GLYMA11G00640.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0020g02960.t01 (Vitis vinifera), 3'ss of exon 10
ctgtaaacattaataattggtttgtacttcctt--ctatgcttacctaattcttgggaactcgttttacaaactttttactaatctagagaccaatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAATGTTGTAACCATCCCTACCTCTTTGTGGGTGACTATGATATCCATAAACA
 || || |||   |||    | | ||||| |    |||  | ||  || ||   |  |            | || ||||||||   | ||  | || || ||| ||||| || ||||||||| |||||||| || | |||||||||||||| ||||||||||| || ||||| ||||| || || ||| |||||    |  |
-tgaaatcatgtttaacct-tctatacttgccaaactagtcataattacttgccgaaagagaaaacctgcacctgtttactaaaacaaagtacgatttgcagGATCTGGGAAGTCAAAAAGTTTACAGAACCTGTCCATGCAACTCAGAAAGTGTTGTAACCACCCATACCTATTTGTTGGAGATTATAATATCTGGCAGAA
















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|193546601|gb|FK500076.1|FK500076
EST:     AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATG                         GTTCTAGGAAAATACAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAA
genomic: AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCT-GGAAAAT-CAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAA
EST: gi|193538092|gb|FK498067.1|FK498067
EST:     AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATG                         GTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
genomic: AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
EST: gi|208289634|gb|GE088517.1|GE088517
EST:     AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATG                         GTTCTGGAAAATCAAAAAGT
genomic: AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCTGGAAAATCAAAAAGT
EST: gi|193661222|gb|FK607454.1|FK607454
EST:     AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATG                         GTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
genomic: AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
EST: gi|207806949|gb|GD778838.1|GD778838
EST:     AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATG                         GTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
genomic: AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
EST: gi|6341769|gb|AW164518.1|AW164518
EST:     AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATG                         GTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
genomic: AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
EST: gi|18730571|gb|BM525953.1|BM525953
EST:     AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATG                         GTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
genomic: AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
EST: gi|193567116|gb|FK523327.1|FK523327
EST:     AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATG                         GTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
genomic: AGTATATTATCAACAAGTCACTGATGTTGGCAGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
EST: gi|193655607|gb|FK606207.1|FK606207
EST:     AGAGTTGGCTTAGACAATG                         GTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT
genomic: AGAGTTGGCTTAGACAATGgtttgtacct ... caatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcttgggaactcgttttacaaactttttactaatctagagaccaatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAATGTTGTAACCATCCCTACCTCTTTGTGGGTGACTATGATATCCATAAACA
                              tactaat  putative branch site (score: 1)
                ttttacaaacttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtaaacattaataattggtttgtacttccttctatgcttacctaattcttgggaactcgttttacaaactttttactaatctagagaccaatctgtagGTTCTGGAAAATCAAAAAGTCTACAGAACTTGACAATGCAACTCAGAAAATGTTGTAACCATCCCTACCTCTTTGTGGGTGACTATGATATCCATAAACA

- - - - - - - - -tggtttg
- - - - - - - - - - - - - cttcctt
- - - - - - - - - - - - - - - - -ctatgct