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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacatatgctaatttggtagtttgggttcttgttttacttgaagcacaggtgtgcagctgtaaatgctaattttactaattatgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA

Basic information

species Glycine max
transcript GLYMA17G11600.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g09130.1 (Oryza sativa), 3'ss of exon 2
tacatatgctaatttggtagtttgggttcttgttttacttgaagcacaggtgtgcagctgtaaatgctaattttactaatt--atgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
  |   |   |  ||   |||| ||         | |   |     ||| |     |   |  | |    | | ||  | |  ||   ||| |      ||||| ||||||||||| ||||| |||||||| ||| | |  ||||| || |||||| |||||||||||||||| |||||||| |||||||||||||||||||
--ccggtttgatcttaaaagttgggcagaaaaagtcaagagtcagtcagttaccttgtatttgaagtatttctgacggaatccatctgttgttataccacagACTACACATGTTGCAGCACAGTATGGTCAAACATCATATCTTTATCATATTGTTGCAAAATGGAATGCTGATCCTGATGTCCCTGATAATGATGGAAGAA

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 2
---tacatatgctaatttggtagtttgggttcttgttttacttgaagcacaggtgtgcagctgtaaatgctaatt--ttactaattatgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
   |  |  |   ||||   ||| |    |    |     |  ||| ||      |    || |    |  ||||  |||  || | |    |||| |  ||||| ||||||||||||| || || ||||| |||||||| ||  |||| || |||||| | || ||||||||||| || ||||| |||||||||||||||||||
aatttaacctatgaattctctaggtaaaat----gaaaagcaagaatcaacaacttttgtctatggcagtgaatttgttaaaaactctatactgct-gtttgcagGCAACACATGTTGCAGCGCAGTATGGCCAGACAGCATTTATTTATCATATTGTTGCGAAGTGGAATGCTGATCCAGATGTCCCTGATAATGATGGAAGAA

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G087806_T01 (Zea mays), 3'ss of exon 2
tacatatgctaatttggtagtttgggttcttgttt-tacttgaagcacaggtgtgcagctgtaaatgctaattttactaattatgatttgctt--ggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
  ||| || |  ||  ||  |  |||          || ||||||      | |||||  | |  ||  |    |  | |||  ||| | |||  |  | ||| | || |||||||| ||||| ||||||||||| || ||| |||||||||||||| |||||||||||||||| || ||| | ||||||||||||||||| |
-tcatgtgattgttctgtgttaagggaaaaaaagaataattgaagt-tgattatgcaga-gaatttgtcacagctctttatttcgatatacttctgtgttcagGCCACGCATGTTGCAGCACAGTATGGTCAGACTGCATTCATTTACCACATTGTTGCAAAATGGAATGCTGATCCAGATATCCCTGATAATGATGGAAGGA

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G024437_T01 (Zea mays), 3'ss of exon 2
--tacatatgctaatttggtagtttgggttcttgttttacttgaagcac-aggtgtgcagctgtaaatgctaattttactaattatgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
    ||| || |  ||   |  |  ||      |    | |  |      | |     |  | |  |      ||| | ||| |||  ||    ||  | ||| | ||||||||||| ||||| ||||||||||| || ||| |||||| ||||||| | |||||||||||||| || ||| | |||||||||||||| || |
ttgtcatgtgattgttccatgttagggaaaaaagaaccagtgaagttgttatgcagagaatttttcacagctctttaagtaaatatatttc---tgtgttcagGCCACACATGTTGCAGCACAGTATGGTCAGACTGCATTCATTTACCGCATTGTTGCGAAATGGAATGCTGATCCAGATATCCCTGATAATGATGGGAGGA

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------tacatatgctaatttggtagtt-tgggttcttgttttacttgaagcacaggtgtgcagctgtaaatgctaattttactaattatgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
                          | ||| | ||    ||     | |    | |   ||   ||   |   || | |  |   ||  ||| ||||  |  ||||| |||  ||||||     || ||||||||||||| ||||| ||||| ||||| ||||| ||||  ||| |||| ||||| ||||||||||| ||||| || |||||||||||||||||||
gttcatatctcttctttaactacgcgtccatgttctctgctgacttctatcaaatttcccttcttttcttgtttagttctcaatgggtgtatgttaatact--taattttgaactgcttg----tagGCAACACATGTTGCCGCACAGTATGGCCAGACTGCTTTTCTTTGTCACGTTGTCTCAAAGTGGAATGCTGATCCTGACGTGCCTGATAATGATGGAAGAA

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
-tacatatgctaatttggtagtttgggttct-tgttttacttgaagcacaggtgtgcagctgtaaatgctaattttactaattatgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
 | || ||  || ||   ||   || ||| | |||  | ||   |        | ||      | ||  ||||     || |||   | | ||    ||||||||||||||||||| |||||||||||||| || |||||||| |||||| ||||| |||||||||||||||| ||||||||||||||||||||||||||||
attca-attttatttctctatcctgtgttgtatgtgcttctcatattggcatcgggctttgtcatattttaatgggtttatttactctct-ctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA

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|254317845|gb|GR826829.1|GR826829
EST:     TACTCCAGGAGGGTGCTCGAGTGAGTGCTGCCGATATGAATGGATATCAG                         ACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATT
genomic: TACTCCAGGAGGGTGCTCGAGTGAGTGCTGCCGATATGAATGGATATCAGgttagattgg ... ttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaggtgtgcagctgtaaatgctaattttactaattatgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
                            tactaat  putative branch site (score: 1)
                                        tttgctt  putative PPT
               taaatgctaattttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacatatgctaatttggtagtttgggttcttgttttacttgaagcacaggtgtgcagctgtaaatgctaattttactaattatgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- catatgc
- - - - - - - - - -gtttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg