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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagcaattctaataagaaaagtttaaaagtttaagttaatggcaaattggcaatcaacaatgacgataataatgttttgttttaaaaaatgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGGACAAAGATGGTGACTGGATGCTCGTTGGAGATGTCCCTTGGGA

Basic information

species Glycine max
transcript GLYMA13G43780.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43780.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G15540.1 (Arabidopsis thaliana), 3'ss of exon 1
actagcaattctaataagaaaagtttaa--aagtttaagttaatggcaaattggcaat-caacaatgacgataataatgttttgttttaaaaaatgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGGACAAAGATGGTGACTGGATGCTCGTTGGAGATGTCCCTTGGGA
   | || || ||       |   ||||  |   ||   |  ||  | |||| || ||   |  |  || ||  |||  ||   | |  | | || |   |||| |  || ||||| ||||  || ||    ||| ||||| |||||||||| ||||||||||| |||||||||||||  || ||||| ||||||| 
---accacttgtatagttgtattgttaattagacttttctatataccgaattcgccatattatcaacacaattttaaatttacatatatacatatttgtgcagGTGTGGCCTTGAAAGATGGTGACAACTGCGAATACGTTACCATATACGAAGACAAAGATGGAGACTGGATGCTCGCCGGTGATGTACCTTGGGG

upper sequence: GLYMA13G43780.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G52830.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------------------actagcaattcta---ataagaaaagtttaaaagtttaagttaatggcaaattggcaatcaacaatg-acg-ataataat----gttttgt----tttaaaaaatgttgaca--------gGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGGACAAAGATGGTGACTGGATGCTCGTTGGAGATGTCCCTTGGGA
                                                                     |||  || | ||   ||| | |  |||      | ||  |  || | || |  | |   |  ||   ||  ||| || |      ||| |    | ||| | ||||  | |        |  | || |  |||||| |   ||||   |||| || ||   |||||||| ||||| ||| | |||||||||||||| |||||||| |||||| |
gttagtaatggcatggactaatttcccgtaacgttagttaatagttacatgaccatgtttataattgagctataaactttatatatacgtattgttagggtttctatatatattggaagtgtgaagagagtaaaacacatatattagttggaactttatgaaatataacacatgtatatataaactatgcagGAGTGGCGAAGGAGGGTAAGAAGTGTGAATACATTATTATATACGAAGACAAGGATAGAGACTGGATGCTCGTCGGAGATGTACCTTGGCA

upper sequence: GLYMA13G43780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g05150.t01 (Vitis vinifera), 3'ss of exon 1
-actagcaattctaataagaaaagtttaaaagtttaagttaatggcaaattggcaatcaacaatgacgataa--taatgttttgttttaaaaaatgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGGACAAAGATGGTGACTGGATGCTCGTTGGAGATGTCCCTTGGGA
 |  |||   | |  |  || |  | | | | |  || |  |||||       |||  | |  ||| ||  |  ||||  |||  || || |  ||||| |||| ||||| ||||| ||||| || | | | ||  |  |||||||||| |||||||||||||| ||||||||||| || |||||||| ||||||||
gatgagcgtattt--ttcgagatttatgataatcaaaatctatggctccaccacaaa-acccttgaagaagaactaattcttttgttaaatatgtgttggcagGTGAAGCATTGAAAGATGCAGATAGTTCAGAGTATATTCCCATATATGAGGACAAAGATGGGGACTGGATGCTTGTAGGAGATGTTCCTTGGGA

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|208034831|gb|GD835945.1|GD835945
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAAACAACGTTACCCAATATAC
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAA-CA-CGTT-CCCA-TATAC
EST: gi|298166128|gb|HO009099.1|HO009099
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|7234689|gb|AW570024.1|AW570024
EST:     GAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: GAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|16347647|gb|BI973242.1|BI973242
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|298182429|gb|HO026604.1|HO026604
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|192327356|gb|FK019573.1|FK019573
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|298182687|gb|HO031422.1|HO031422
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|298184244|gb|HO029457.1|HO029457
EST:     TTCGAAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTCCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|151396542|gb|EV266419.1|EV266419
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|193670201|gb|FK613207.1|FK613207
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATG
EST: gi|151393526|gb|EV263401.1|EV263401
EST:     TTCAGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|17021052|gb|BM092086.1|BM092086
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|151394409|gb|EV264280.1|EV264280
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTACGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|151411232|gb|EV281043.1|EV281043
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|193552402|gb|FK510321.1|FK510321
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGGGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|151397845|gb|EV267718.1|EV267718
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|298188539|gb|HO035232.1|HO035232
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|192325700|gb|FK015057.1|FK015057
EST:     TTCGGAGCTGGTCTTGACCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|151405648|gb|EV275462.1|EV275462
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|8827402|gb|BE211132.1|BE211132
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|15813012|gb|BI785287.1|BI785287
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
EST: gi|298198357|gb|HO039896.1|HO039896
EST:     TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTC                         GCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG
genomic: TTCGGAGCTGGTCTTGGCCTTGGAGAAGTTCTTCGGTTGCTATGGAATTCgtaagttatt ... atgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattggcaatcaacaatgacgataataatgttttgttttaaaaaatgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGGACAAAGATGGTGACTGGATGCTCGTTGGAGATGTCCCTTGGGA
                      ataataatgttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagcaattctaataagaaaagtttaaaagtttaagttaatggcaaattggcaatcaacaatgacgataataatgttttgttttaaaaaatgttgacagGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGGACAAAGATGGTGACTGGATGCTCGTTGGAGATGTCCCTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -gcaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgac