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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaatatatagttgagaattttgtatccgtatatgaaattttcttatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaatagGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC

Basic information

species Glycine max
transcript GLYMA10G10180.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 8
aaaaatatatagttgagaattttgtatccgtatatgaaattttcttatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaat---agGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
    ||  | | || |       |  |   ||| |    | | |||  || |||||     | | |     |||  |||| ||     ||   |||||   |||| ||||| || ||||| || || || |||||||| || || ||||||||||||||| | |||||||||||||| ||| | || |||||  | |||||||
-ctgatgca-atttaatgcacccgattgtttattttttgtatgcttgaatgcttccattttagttgca-ttttgaatttactgaaacagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGACGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTGCGTGACC

upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 1
aaaaatatatagttgagaattttgtatccgtatatgaaattttcttatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaat---agGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
    ||  | | || |       |  |   ||| |    | | |||  || |||||     | | | |   |||  |||| ||   | ||   |||||   |||| ||||| || ||||| || || || |||||||| || || || |||||||||||| | |||||||||||||| ||| | || |||||  |||||||||
-ctgatgca-atttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcg-ttttgaatttactgaaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC

upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 6
---aaaaatatatagttgagaattttg-tatccgt-atatgaaattttcttatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaa---tagGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
   | | | |  || |  |  | |    ||  | | | ||| | ||    |||  | ||   |||  ||  |  | |||   |  | |  |   ||||| ||    || |  | || ||  |  | |     || || |||||||| ||||| || ||||| |||||||||||||||||||| ||| || | || ||  |||| || |
gtaagatacaactattctactactcaactactcatcacatgtagttgaagtatgatattttaagcttct--ttactttgaaat-gtcgaatcaattgttgaaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC

upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 6
aaaaatatatagttgagaattttgtatccgtatatgaaattttcttatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaata--gGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
    || |  ||       | ||||||  | |||      |  |  | |  | | ||      |  |   |   | | |  ||  |||| |||||||||  ||| || ||||||||  | |  ||||| || |||||||| ||||| |||||||||||||||||||||||||| |||||  |  | |||||||| | |||||
tgtcatttgaaggattagttgttgtataagcatactgggatggc--acacacattctgatgttttcttttccattctcttatgattttgatgttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATTCATGAAAGAGGCATGAATGAGGACTTCCTTTTAATAATTTTGCATGACC

upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S36_206V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------aaaaatatatagttgagaattttgtatccgtatatgaaattttcttatattcttcctagcaactagt-ggccttgtttttattgtctttgttgttaaatagGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
                                                          | ||  | |  || | ||      | | | || ||   |   ||    |  | | |  | | |   |   |   ||  | |  | ||  |||  |||||| ||||| || |||||||  ||||| |||||| |  |||| ||||||||||||||| | |||||||||||||| || ||| | || |||||||| || |
gtacgttctgtgccttatattacgaacttggagattctttttcattgtatgattgtctagtacttggcagaaatttgcagtgcagaagatcaatggtaggtaggaaccacttcgtcatttgccagtactaacttgttggcatgtggggttgcatagGTCCAAGAGCCTGACTTGAATGGTGTGAGTCATGTCATGGTTGACGAAATTCATGAACGCGGCATGAATGAAGATTTCTTATTGATCATTTTACGAGATC

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|14125758|gb|BG790196.1|BG790196
EST:     CAGAAACACGCCTTCTTTTCTGCACCACTGGTGTATTACTTCGGCAGTTG                         GTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGGTG-ACGAAAT
genomic: CAGAAACACGCCTTCTTTTCTGCACCACTGGTGTATTACTTCGGCAGTTGgtaatattag ... tgttaaatagGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGG-TGGACGAAAT
EST: gi|193680412|gb|FK623576.1|FK623576
EST:     CAGAAACACGCCTTCTTTTCTGCACCACTGGTGTATTACTTCGGCAGTTG                         GTACAAGACCCAGACTTGACT-GGTGTTAGTCATTTGCTGGTGGATGAAAT
genomic: CAGAAACACGCCTTCTTTTCTGCACCACTGGTGTATTACTTCGGCAGTTGgtaatattag ... tgttaaatagGTACAAGACCCAGACTTGA-TAGGTGTTAGTCATTTGCTGGTGGACGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaatagGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
                                      tctttgtt  CT-rich tract
                             tttttattgtcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaatatatagttgagaattttgtatccgtatatgaaattttcttatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaatagGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctttg