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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattaaaaaaccgatagcacagtctactgcttatatttttattactctgttgcaattttttttactgttttgatacaaaggtgtgctgcattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAGCCCGAGAGATCAGTTCACAACCACCCTACACTGAGTATGTCTCCACACG

Basic information

species Glycine max
transcript GLYMA01G35190.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 5
aatattaaaaaaccgatagcacagtctactgcttatatttttattactctgtt---gcaattttttttactgttttgatacaaaggt-gtgctgcattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAGCCCGAGAGATCAGTTCACAACCACCCTACACTGAGTATGTCTCCACACG
  |||| | |    | |   | ||| |      |||   | |   | |||| |     || |   | | |  |    || |     | ||       ||| |||| |||||| ||||||| || ||| | || ||||| ||||||||||| || || || ||||||| ||| |||||||| ||||| || |||||||| |||||
--tatttatatgtgggt--tatagtttctcaaatatgcatcttccattctgattaaaaaaatgcatcttccataaaaattccttccttgtatgtttcttttcagAGAACTTGTTGGTTACAAAAGATGTAATAAAAATTGCTGATTTTGGTCTTGCTCGGGAGATCAATTCTCAACCACCATACACGGAATATGTCTCTACACG
















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|7589585|gb|AW705356.1|AW705356
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|254336468|gb|GR842647.1|GR842647
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|254345622|gb|GR855958.1|GR855958
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|14205773|gb|BG839451.1|BG839451
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|193479799|gb|FK445480.1|FK445480
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|193578725|gb|FK535299.1|FK535299
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|192299757|gb|FG990052.1|FG990052
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|26048711|gb|CA785164.1|CA785164
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGTTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|22522544|gb|BU081355.1|BU081355
EST:     CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
EST: gi|298163466|gb|HO012199.1|HO012199
EST:     CATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTG                         AAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG
genomic: CATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgtacttattt ... cattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctgttgcaattttttttactgttttgatacaaaggtgtgctgcattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAGCCCGAGAGATCAGTTCACAACCACCCTACACTGAGTATGTCTCCACACG
                        ttttgat  putative branch site (score: 4)
          aattttttttactgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattaaaaaaccgatagcacagtctactgcttatatttttattactctgttgcaattttttttactgttttgatacaaaggtgtgctgcattttgcagAAAACTTGCTGGTTACCAAGGATTTTATCAAAATCGCTGATTTTGGCCTAGCCCGAGAGATCAGTTCACAACCACCCTACACTGAGTATGTCTCCACACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA