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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgttggagaaagtagttggttttcttttatggatttctctgatttatttgtagttaatagatggtcttgagttaacatggtatgatacaatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTTGACATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT

Basic information

species Glycine max
transcript GLYMA18G49660.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49660.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G01120.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagtgttggagaaagtagttggttttcttttatggatttctctgatttatttgtagttaatagatg-gtcttgagttaacatggtatgatacaatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTTGACATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT
                   ||  ||| | |   ||   | ||  |  |  | ||| |   |    ||| ||||  | || |    |  |  |         ||||| ||||| |||||||||||||| || || || |||||||| |||||||| |||||| |||| |||||| |  | |||||||||| ||| ||| || | |
-------------------gtcagttctgtaacattattgtcctttttacagttggaaagagagtatgtgtctcaaatttattccgacttgtctgg-----cagGTATCTCTGTTCTTCACTGAGTCCCCGACAAACCCATTCCTTAGATGTGTCGACATTGAGCTAGTTTCAAAAATATGCCACAAGAGGGGAACTCTGGTTT

upper sequence: GLYMA18G49660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 5
gttagtgttggagaaagtagttggttttcttttatggatttctc--tgatttatttgtagttaatagatggtcttgagttaacatggtatgatacaatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTTGACATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT
|| ||| ||  |||  || ||| |||||      |    || ||  | ||   |||  |  |   || |  |  |||| | || ||  ||  | ||  ||| |||||  | || |||||||||||||| || ||||||||||| || ||||||||||||||| || ||||||||||||||||||||| ||||||  |  |  |||
gtcagtattcaagatggttgttagtttttcgaagttttcttttcagtaatcatttttcaaatggcaggtcatactgagatgac-tgacattgt-ca--catgcagGTTACACTTTTCTTCACTGAGTCTCCGACCAATCCATTTCTCAGATGTGTTGACATTGAGTTGGTTTCAGAGCTTTGCCACAGGAAGGGAGCACTAGTCT
















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|120492993|gb|EH221160.1|EH221160
EST:     TGATCCAGCAGATGTTGGAGCCATTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TGATCCAGCAGATGTTGGAGCC-TTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|254343496|gb|GR857252.1|GR857252
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|21993909|gb|BQ785437.1|BQ785437
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|24136385|gb|BU926895.1|BU926895
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|192322238|gb|FK014134.1|FK014134
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|192319773|gb|FK013787.1|FK013787
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|37996373|gb|CF807962.1|CF807962
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|13791349|gb|BG653940.1|BG653940
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|254314402|gb|GR831987.1|GR831987
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|6072565|gb|AW101952.1|AW101952
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTTTAATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcattcagGTGTCTCT-ATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgtagttaatagatggtcttgagttaacatggtatgatacaatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTTGACATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT
                          agttaac  putative branch site (score: 3)
       tagttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgttggagaaagtagttggttttcttttatggatttctctgatttatttgtagttaatagatggtcttgagttaacatggtatgatacaatcattcagGTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTTGACATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG