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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatcctttctctctcaattcatcaaagtttcaatcttttttctaatggggtctcttcctgattctgggtcctctttgtcttttgttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA

Basic information

species Glycine max
transcript GLYMA09G39370.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39370.4 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
---gttaatcctttctctctcaattcatcaaagt-ttcaatcttttttctaatggggtctcttcctgattctgggtcctctttgtcttttgttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA
    ||  ||  || ||      | | | |  || |||    |  ||| |  |  | |||   | |  ||   ||   |||| || | | |   || | ||||||||||| || ||||||||||||||| | || ||||| ||||| ||||| |  ||  ||||| | || ||    || |
tctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtc-gcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: GLYMA09G39370.4 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T05 (Zea mays), 3'ss of exon 1
--------gttaatcctttctctctcaattcatcaaagtt-tcaatcttttttctaatggggtctcttcctgattctgg-gtcctctttg--tcttttgtttt-------ccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA--------------------
        | |   ||| |||   ||  ||   |||   |  |   |  | ||||  | |  | | ||  ||||   |   | ||    |  | | ||| |||        || ||||||||||| || ||||||||||||||| | || ||||| ||||| ||||| |  ||  ||||| | || ||    || |                    
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA

upper sequence: GLYMA09G39370.4 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
--------gttaatcctttctctctcaattcatcaaagtt-tcaatcttttttctaatggggtctcttcctgattctgg-gtcctctttgtctt--ttgtttt-------ccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA
        | |   ||| |||   ||  ||   |||   |  |   |  | ||||  | |  | | ||  ||||   |   | ||    | |||  ||| |||        || ||||||||||| || ||||||||||||||| | || ||||| ||||| ||||| |  ||  ||||| | || ||    || |
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: GLYMA09G39370.4 (Glycine max), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
--gttaatcctttctctctcaattcatcaaagtttcaatcttttttctaatggg--gtctcttcctgattctgggtcctctttgtcttttgttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA
   ||      |  |  ||    |  |   | ||       |||    ||| ||     | ||  ||  ||||     ||       | || ||   |||||||||||||||| ||||||||||||||| | ||||||||||||   ||||| |||||| | || ||||||||   ||| |
ggattgtgttgtgattacttttcttgttcgaattggtgcggtttggggaatcggcaagttgttgttgtatctgacgattcaagaatgtgtgattgg-gtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA

upper sequence: GLYMA09G39370.4 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------gttaatcctttct---ctctcaattcatca--aagtttcaatcttttttctaatggggtctcttc-ctgattc--tgggtcctctttgtcttttgttttccgt-----agGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA
                        | ||| | ||||   ||||| | |    |  ||    |  ||||| |||   |     ||||   || ||||  ||  || ||||| |  ||    ||||       |||||||||||||| |||||||| |||||| | || ||||| ||| | || ||| ||||| | |||||||||||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: GLYMA09G39370.4 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
-------------------gttaatcctttctctctcaattcatcaaagtttcaatcttttttctaatggggtctcttc-ctgattc--tgggtcctctttgtcttttgttttccgt-----agGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA
                   |    ||  |||  |||    ||  ||  |   |  ||||| |||   |     ||||   || ||||  ||  || ||||| |  ||    ||||       |||||||||||||| |||||||| |||||| | || ||||| ||| | || ||| ||||| | |||||||||||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

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|298176485|gb|HO026720.1|HO026720
EST:     AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|151393517|gb|EV263392.1|EV263392
EST:     GAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: GAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|254327210|gb|GR836819.1|GR836819
EST:     GAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: GAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|192294831|gb|FG987520.1|FG987520
EST:     GAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: GAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|151395834|gb|EV265711.1|EV265711
EST:     ATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: ATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|298193444|gb|HO033878.1|HO033878
EST:     AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGGTGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|298195504|gb|HO043895.1|HO043895
EST:     AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGATGAGCGATTACAAGGTCGAGGTGATTAATGATGGTATGCAAGAATT
genomic: AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|7924716|gb|AW830742.1|AW830742
EST:     TCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: TCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|17020964|gb|BM091998.1|BM091998
EST:     AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
EST: gi|298191356|gb|HO038835.1|HO038835
EST:     AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGGTGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT
genomic: AGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctt ... ttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaatggggtctcttcctgattctgggtcctctttgtcttttgttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA
                             tcctctttgtcttttg  CT-rich tract
                                        ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatcctttctctctcaattcatcaaagtttcaatcttttttctaatggggtctcttcctgattctgggtcctctttgtcttttgttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA