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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacaccaaatatgttactattattttgtggtggtcatcaactatgctacaatgtaacaagctattcagtcatttagttattaaaatctgattcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG

Basic information

species Glycine max
transcript GLYMA03G34300.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------------ttacaccaaatatgttactattattttgtggtggtcatcaactatgctacaatgtaac--aagctattcagtca-------tttagttattaaaatctgattctt-----------gtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG
| | | | | | |||| | ||| | ||| | | | || || | | | |||| || ||| ||| | || || | | | || || || || |||||||| || | || || | |||||| |||||||||| |||||||| |||||| ||||||| ||||||||||||
gttgggtacactggacactgagcacccttttctttgctaactatatacatagagattgcaactatctgtaaagcggttataaaatccagtctgttggttttactggatggactttgtataatagttaacgagggattgggagctttttcttcacttctggttttgctaatagagttttatctttcccttaaaattacagTGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG

upper sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------ttacaccaaatatgttactattattttg-tggtggtcatcaactatgctacaatgtaacaagctattcagtcatttagttattaaaat--ctgattct----tgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG
|| | || || ||| | | | | | | | ||||| | | | | | | | | ||| | | || | | |||| |||||| || ||||| ||||| ||||||||||| ||||||| ||||| || || |||||||| || |||||||| ||||||
gttacgacttctctttttcacttatactatatctctttttatttgattgaaattttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaacc--ttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG

upper sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 4
ttacaccaaatatgttactattattttgtggtggt-catcaactatg-ctacaatgtaacaagct-attcagtcatttagttattaaaatctgattcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG
| || | || | | | || | | | | || | ||| || || | ||| || | |||| || | ||| ||| | ||||| | ||||||| | |||||| |||| ||||| |||||| | ||||| || |||||| | |||||||||||||| ||| ||||| ||
atgttccgattacagttttttgcttgcattattgcacttctcccatgtcttcactctaatgttcttgtacagttatcaatttacctttatcc---tgatgtagTGTGGAACAATTGAAAGATATTGGCTGCAACTGGGTTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG

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|16281659|gb|BI944602.1|BI944602
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|151395984|gb|EV265861.1|EV265861
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|209724178|gb|BW659712.1|BW659712
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|20813031|gb|BQ297509.1|BQ297509
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTG
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTG
EST: gi|4314103|gb|AI461222.1|AI461222
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|20449041|gb|BQ253165.1|BQ253165
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|15204096|gb|BI426864.1|BI426864
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|10233567|gb|BE802455.1|BE802455
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|20449080|gb|BQ253204.1|BQ253204
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|9204176|gb|BE330400.1|BE330400
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTT-ACTGGAGAAATCAG                         CGCGGAACAACTAACAGATCTTGGATGCAAGTGGGTTGGTCTGGG-CATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|120530487|gb|EH258620.1|EH258620
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|9563997|gb|BE473506.1|BE473506
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTACAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|209715618|gb|BW657385.1|BW657385
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
EST: gi|17964485|gb|BM271219.1|BM271219
EST:     GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAG                         CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC
genomic: GCCCAGAATTCTTGGGTTGGAAAAGGTGGTGCTTTTACTGGAGAAATCAGgttagcttgt ... attcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacaatgtaacaagctattcagtcatttagttattaaaatctgattcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG
                                              ttcttgt  CT-rich tract
 atttagttattaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacaccaaatatgttactattattttgtggtggtcatcaactatgctacaatgtaacaagctattcagtcatttagttattaaaatctgattcttgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- -caccaaa
- - - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - -catcaac
- - - - - - - - - - - - - - - - - - - - - - tgctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagcta