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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacttactcaagttgatttttgacaatttgatttgatgggatcaatggtgactgacatttatctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT

Basic information

species Glycine max
transcript GLYMA05G36620.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 2
---------gtaagacttactcaagttgatttttgacaatttgatttgatgggatcaatggtgactgacatttatctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT
          |    | ||  |  | |  | |||     | |   |   ||    |     ||||    ||   | || ||||||||| ||||| ||||||||||| || || ||||| ||||| || || |||||||| |||||||| || || || ||||| || || || || |||||||| 
gtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGATTGTGAACAAGGACGGTAAGCCCTACATTCAGGTCAAGATCAAGGATGGA

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaag-acttactcaagttgatttttgacaatttgatttgatgggatcaatggtgactgacatttatctttttg-cagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT
||||  ||||| ||    || || ||     || ||  ||||    |   |           ||  | | |||| ||| || || |||||||| |||||||  |||| ||| ||||| |||||  ||||||| ||||||||||| || || ||||| ||||| || || |||||||||
gtaattacttattctctgtgtttgtttcaccttggagatgatattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 2
-------gtaagacttactcaagttgatttttgacaatttg-atttgatgggatcaa--tggtgactgacatttat-----ctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT
       ||    ||  || ||| |  |  |  |    ||| ||| | ||| |   |  |  |  ||||   || |     |||||  |||||| ||||||||||| ||||| |  || |||||||||||||| || || ||||| ||||||||||| || |||||||| ||||| || || |||||||||
gtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACATTGTTAACAAGGATGGGAAGCCTTACATTCAAGTCAAGATCAAGGATGGT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 2
---------------gtaagacttactcaagttgatttttgacaat---ttgatttgatgggatcaa----------tggtgactgacattta--tctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT
                | |  ||   |   ||| || || |   ||   |||| |  |    |||||          ||||   |  | |||   | ||| || || || || ||||| || |||||||  || ||||||||| | || |  ||||| || |||||||||||||| || || |||||||| || ||||||||||| 
gtatgtgataaatcctttaatctcctttctgttcatattcgttgatcttttgaatgaagcccatcaaggctctaacctggttttttgccttttgttttttctgtagATTTGATGATAAAGAGGTTCAAAAGGACATGAAGCTTTTCCCATTCAAGATCGTGAACAAGGATGGAAAGCCATATATACAAGTCAAGATTAAGGATGGG

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 2
gtaagacttactcaagttgatttttgacaatttgatttgatgggatcaatggtgactgacatttatctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT
       | | | |  ||    |||| ||||||    |  | |   |        || ||  |  |    |  |||||| ||||| || || ||||||| ||||||||||||  |||| | |||||| |||||||||||||||||||| ||||| ||||| ||  | |||||||| 
------gtaagttagattcccatttg-caatttttcctacttgttccttcttgatctaactctcgtaccgtcacagGTTTGAAGACAAAGAGGTTCAAAAAGATATGAAGCTCTTTCCATTTAAGATCGTCAACAAGGATGGAAAACCGTACATCCAAGTCAAGGTGAAGGATGGC

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 2
gtaagacttactcaagttgatttttgacaatttgatttgatgggatcaatggtga-ctgacatttatctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT
             |||||   ||    | |||||   |  |    ||  |  ||| || ||  |  |    |   ||||| ||||| || || ||||||||||||||||||||  |||| | |||||| |||||||||||||||||||| ||||| ||||| ||  | |||||||| 
-----------gtaagttagattc---ccatttgcaatttttccttccttcttgatctaactctcgtaccgtcatagGTTTGAAGACAAAGAGGTTCAAAGAGATATGAAGCTCTTTCCATTTAAGATCGTCAACAAGGATGGAAAACCATACATCCAAGTCAAGGTGAAGGATGGC

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|9986537|gb|BE660645.1|BE660645
EST:     GTCAACCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAA                         GTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGAT
genomic: GTCAACCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaagactta ... ctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgacaatttgatttgatgggatcaatggtgactgacatttatctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT
                                gactgac  putative branch site (score: 2)
                                        tttatcttttt  CT-rich tract
                                     acatttatcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacttactcaagttgatttttgacaatttgatttgatgggatcaatggtgactgacatttatctttttgcagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG