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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttatctgctactcttagtcttagattctcatcaattttcagttgcatcagtgacagattttatattgaatcttatatggttttttggttctcgtccagCTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATTTTGGGAATTGCTGCTTATTTGTACAA

Basic information

species Glycine max
transcript GLYMA03G33680.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33680.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0040g02130.t01 (Vitis vinifera), 3'ss of exon 7
gttttttatctgctactcttagtcttagattctcatcaattttcagttgca-tcagtgacagatt-ttatattgaatcttatatggttttttggttctcgtccagCTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATTTTGGGAATTGCTGCTTATTTGTACAA
| || || | ||| |||||||| ||| || || || ||| ||||| | || | |||| | | | ||||||| | | ||||| | ||||||||||| || || ||||||||| |||||||| ||||||| ||||||||||||| ||| | || ||
----gtaatttgactattttaagcttagatttccatttatcctctcctgtgctcatctgtagattactctactagatctaacaaagggttttggtattgcttcagCTGAGGTCCAGTCGAAATTTCTGCATTGATATTATTTTGTTGTGTATAATTCTGGGAATTGCTGCCTATCTATATAA
















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|193393088|gb|FK358380.1|FK358380
EST:     AATGTTAGACTTAGAGATACAGTGAACCAG                         CTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATT
genomic: AATGTTAGACTTAGAGATACAGTGAACCAGgttttttatc ... tctcgtccagCTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATT
EST: gi|19053265|gb|BM731932.1|BM731932
EST:     CTTCTGACCTTAAAAATACCAATGTTAGACTTAGAGATACAGTGAACCAG                         CTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATT
genomic: CTTCTGACCTTAAAAATACCAATGTTAGACTTAGAGATACAGTGAACCAGgttttttatc ... tctcgtccagCTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATT
EST: gi|31471750|gb|CD413778.1|CD413778
EST:     CTTCTGACCTTAAAAATACCCATGTTAGACTTAGAGATACAGTGAACCAG                         CTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATT
genomic: CTTCTGACCTTAAAAATACCAATGTTAGACTTAGAGATACAGTGAACCAGgttttttatc ... tctcgtccagCTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatcagtgacagattttatattgaatcttatatggttttttggttctcgtccagCTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATTTTGGGAATTGCTGCTTATTTGTACAA
                                            ttctcgtcc  CT-rich tract
 attttatattgaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttatctgctactcttagtcttagattctcatcaattttcagttgcatcagtgacagattttatattgaatcttatatggttttttggttctcgtccagCTTCGATCCAGTCGAAACTTTTGTATTGATATTGTTTTGTTGATTATAATTTTGGGAATTGCTGCTTATTTGTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT