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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatcttttataaatattttatcttctcaatgctgattgtccttgttaatgtaagttgtcttattatatctgcatgtattaatgtatttcttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG

Basic information

species Glycine max
transcript GLYMA19G36860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 2
atgatcttttataaatattttatcttctcaatgctgattgtccttgttaatgtaag----ttgtcttattatatctgcatgtattaatgtatttct---tcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
       |  ||| ||||  |   || |   || ||    ||      |||         |||| |  | ||   |  ||| |||    | || ||   |  | ||||||||| ||||| ||||| ||||||||||||||||| || || || 
-------tagatagatataatcagttatagttgttgtcattctaatccaatagcgacgttttgtatcgtgatcattaaatgcattttactcttactgacttgtgcagTATTGAAGAGGTCGCCTTTAGTTTCAATGGAGGAAAAGACTCCACT

upper sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 2
atgatcttttataaatattttatcttct------caatgctgattgtccttgttaatgtaagttgtcttat-tatatctgc-atgtattaatgtatttcttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
       | | |  ||  ||  |||| |      ||||  |||| ||  || ||  | |   |||    |  | | | | |   | |   || |   |    | ||||| |||| ||||||||||| || ||||||||||||||||||||||| 
-------tgtttggattcttgctcttttgagatgcaataatgatggtt-ttattgttatctattgggaaaagtgtgtttactgagcaaccatttggcttcctcaacagTGTTGAAGAGGTTGCCTTAAGCTTCAATGGAGGAAAGGATTCAACT
















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|14258476|gb|BG881384.1|BG881384
EST:     AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTC                         TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACA
genomic: AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTCgtaagttgtt ... cttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
EST: gi|7691690|gb|AW759813.1|AW759813
EST:     GCTTTGGCTTTGTATTC                         TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
genomic: GCTTTGGCTTTGTATTCgtaagttgtt ... cttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
EST: gi|209709323|gb|BW680988.1|BW680988
EST:     AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTC                         TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
genomic: AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTCgtaagttgtt ... cttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
EST: gi|192299088|gb|FG990402.1|FG990402
EST:     AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTC                         TATGGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
genomic: AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTCgtaagttgtt ... cttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
EST: gi|213614119|gb|DB964891.1|DB964891
EST:     AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTC                         TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
genomic: AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTCgtaagttgtt ... cttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
EST: gi|209727350|gb|BW655281.1|BW655281
EST:     AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTC                         TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGG
genomic: AAGTACAACAACGCTACCTATGTTGTTCAGAGAGCTTTGGCTTTGTATTCgtaagttgtt ... cttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaatgtaagttgtcttattatatctgcatgtattaatgtatttcttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG
                                tattaat  putative branch site (score: 2)
                                        tatttcttcct  CT-rich tract
                             atgtattaatgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatcttttataaatattttatcttctcaatgctgattgtccttgttaatgtaagttgtcttattatatctgcatgtattaatgtatttcttcctacagTATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgta