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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactaagttcaagacaagcttttctgttgatatttttgttctttttgtttctttatggtgaagttgtagaagaaatatgttagaatatgaattcacattacttgataacaattctgtaagttgcaatcatcattatataatgttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATGCTGTAAAAGCCTTCAG

Basic information

species Glycine max
transcript GLYMA07G03660.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03660.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtactaagttcaagacaagcttttctgttgatatttttgttctttttgtttctttatggtgaagttgtagaagaaatatgttagaatatgaattcacattacttgataacaattctgt-aagttgcaatcatcat----tatataatgttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATGCTGTAAAAGCCTTCAG
                                              |  |  |||||||||     |  | |    |   |   ||          || |  || || || ||| ||| | | ||||||     ||| |    |  | |  |  ||||||||||||||| | ||||||||||| |||||||| || ||||| || || | ||||||||||   |||||
----------------------------------------------taatcatttctttat-----aactttcagggctgtgcctt----------tttaacttcctggaaaactattgtattaagttgtttatatcttaccatggacatggcccttgcagATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAG
















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|298163747|gb|HO012480.1|HO012480
EST:     TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATG                         ATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
genomic: TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtacta ... gttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
EST: gi|58016821|gb|CX703563.1|CX703563
EST:     TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATG                         ATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
genomic: TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtacta ... gttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
EST: gi|58023219|gb|CX709960.1|CX709960
EST:     TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATG                         ATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
genomic: TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtacta ... gttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
EST: gi|192295784|gb|FG990850.1|FG990850
EST:     TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATG                         ATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCTTGAACTTAAAAATG
genomic: TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtacta ... gttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
EST: gi|151407112|gb|EV276927.1|EV276927
EST:     TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATG                         ATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
genomic: TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtacta ... gttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
EST: gi|298190883|gb|HO033004.1|HO033004
EST:     TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATG                         ATGTTCCTATTAGTGCTAGAAACATTCTGGAGGATCCTGAACTTAAAAATG
genomic: TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtacta ... gttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
EST: gi|298187580|gb|HO034729.1|HO034729
EST:     TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATG                         ATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
genomic: TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtacta ... gttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
EST: gi|298171416|gb|HO016448.1|HO016448
EST:     TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATG                         ATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG
genomic: TCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtacta ... gttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacttgataacaattctgtaagttgcaatcatcattatataatgttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATGCTGTAAAAGCCTTCAG
      tgataac  putative branch site (score: 2)
                                            tgttctt  putative PPT
                            aatcatcattatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactaagttcaagacaagcttttctgttgatatttttgttctttttgtttctttatggtgaagttgtagaagaaatatgttagaatatgaattcacattacttgataacaattctgtaagttgcaatcatcattatataatgttcttgcagATGTTCCTATTAGTGCTAGAAACATTTTGGAGGATCCTGAACTTAAAAATGCTGTAAAAGCCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG