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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtgaattaattatgagttttgtatttgattgtgttattataaaatctatggttgcattggaacagataatatttgtttttctccatctgtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTATTGAGAGCTTCCCTGATCTTTTCCGTAGCAAATATAATCCATATGATCGC

Basic information

species Glycine max
transcript GLYMA13G34570.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34570.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G16900.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------gagtgaattaattatgagttttgtat--ttgattgtgtta---ttataaaatctatg----gttgcattgg--aacagataatatttgtttttctccatctgtgca-tgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTATTGAGAGCTTCCCTGATCTTTTCCGTAGCAAATATAATCCATATGATCGC
                                   |||       ||  ||  || | |||  ||||       |   |||| | |  | |      |  |  |    |||| | ||| ||| |  || || ||   |  | ||||||||||| |||||  |||| || |||||||||||  ||||||| ||||||||||||| | ||||||| || |||||    || ||||   ||  |||  | 
gtgattttctaagatctttcatcttgtaattttttgagcattcgtatggtggcttctatatcgttgaggaaaccagttttatgatacttttacaaaatcacggtattcaacaaacaatgtttttgattgtcaattaattgactgcagGTTCCTTTATCCTATATACCCTCTTATTTGTGTCTCTGCTTCTGCTGTTATTGAGAACATCCCTGAGCTGTTCCGGGAAAAGTATAGCTCACGTGAAAGT

upper sequence: GLYMA13G34570.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0014g01410.t01 (Vitis vinifera), 3'ss of exon 5
gagtgaattaattatgagttttgtatttgattgtgttat-tataaaatctatggttgc-attggaacagataatatttgtttttctccatctgtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTATTGAGAGCTTCCCTGATCTTTTCCGTAGCAAATATAATCCATATGATCGC
  |   || |        |  | || |     || |     |    ||   ||  ||| | ||    | || |    |  | |  |||   |   | ||||||||||| |||||| ||||||||||| | |||||||||||||||||||| ||||||||||| || |||||||| ||   |  |||  ||||  ||| |  |
--gacgatgatcagaagatcctttaatcccaagtatagggcactttattattgactgccagtgagcaaaatgactgataatatattcccattacccttgcagGTTCCTCTATCCAATATATCCACTTGTCTGTGTTGCTGCTTCAGCTGTCATTGAGAGCTTTCCAGATCTTTTTCGAGACCCATACTATCCCAATGCTAAC
















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|19938576|gb|BQ081785.1|BQ081785
EST:     ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAG                         GTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
genomic: ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAGgtttggctga ... gtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
EST: gi|19053815|gb|BM732482.1|BM732482
EST:     ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAG                         GTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
genomic: ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAGgtttggctga ... gtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
EST: gi|51342060|gb|CO983327.1|CO983327
EST:     ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAG                         GTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
genomic: ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAGgtttggctga ... gtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
EST: gi|208135749|gb|GD933682.1|GD933682
EST:     ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAG                         GTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
genomic: ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAGgtttggctga ... gtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
EST: gi|208306217|gb|GE107838.1|GE107838
EST:     ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAG                         GTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT
genomic: ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAGgtttggctga ... gtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctatggttgcattggaacagataatatttgtttttctccatctgtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTATTGAGAGCTTCCCTGATCTTTTCCGTAGCAAATATAATCCATATGATCGC
                                tttttctccatctgt  CT-rich tract
                    agataatatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtgaattaattatgagttttgtatttgattgtgttattataaaatctatggttgcattggaacagataatatttgtttttctccatctgtgcatgcagGTTCCTGTATCCAGTATATCCACTTATTTGTGTTGCTGCTTCAGCTGTTATTGAGAGCTTCCCTGATCTTTTCCGTAGCAAATATAATCCATATGATCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT