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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattcaaacagtgcctaatcccagacttaattatcttcctttaaaactcccttggtttatgcttttcatttttttcatttgctttttttaatctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCATTATGAGGCAGATTGCTTCAAGTATCACTTATTTGCCATGCCTGGATGAA

Basic information

species Glycine max
transcript GLYMA11G37380.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 4
ttattcaaacagtgcctaatcccagacttaattatcttcctttaaaactcccttggtttatgcttttcatttttttcatttgcttttttta----atctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCATTATGAGGCAGATTGCTTCAAGTATCACTTATTTGCCATGCCTGGATGAA
         ||||   |  |        |   ||  |||     ||  |   ||| ||| |    ||| || |||   | || | | ||||    |  ||| ||||| |||||||| |||||||| |||||||||||||| ||||| ||||| |||||||| ||| ||||||||||| | ||||| ||||| || || ||||||
-------gtcagttttttgtttttagtgttgatactttcgc---aagtttgtttgttttctttgattctttgtttcattatgttatctttatggaactttttagTGTGTCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAA

upper sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0010g02430.t01 (Vitis vinifera), 3'ss of exon 4
------ttattcaaacagtgcctaatcccagacttaattatctt----cctttaaaactcccttggtttatgcttttcatttttttcatttgctttttttaatctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCATTATGAGGCAGATTGCTTCAAGTATCACTTATTTGCCATGCCTGGATGAA
      ||||| |    ||   | ||| |    ||    ||||     || |  |||      ||||||   |||    ||| ||||||||| ||| ||||    ||||| || || ||||| ||||||||||| ||||| ||||||||||||||||| || ||| | ||||||||||| || |||||||||||||||||| | ||||||
gtaatattatt-atctggttttttatctccattttccaaatctcaaaaccctcgaaaggtttctggtttt--cttcatgtttgtttcatttggtttgttta----ttcagGGTGTCAAGGGAGAAGAGTGACAAAGAGATTATGAGAGAGATACAAGCAATCATGCGACAGATTGCTTCCAGCATCACTTATTTGCCATGCATCGATGAA
















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|21595080|gb|BQ610361.1|BQ610361
EST:     GAAAGGTGGAACTTCAGCATTGAGACTGACTGCGAGGTTGTTGAGAAGGG                         TGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCAT
genomic: GAAAGGTGGAACTTCAGCATTGAGACTGACTGCGAGGTTGTTGAGAAGGGgtgggtaact ... aatctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCAT
EST: gi|192309938|gb|FK001482.1|FK001482
EST:     GAAAGGTGGAACTTCAGCATTGAGACTGACTGCGAGGTTGTTGAGAAGGG                         TGTCTCGAGGAAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCAT
genomic: GAAAGGTGGAACTTCAGCATTGAGACTGACTGCGAGGTTGTTGAGAAGGGgtgggtaact ... aatctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCAT
EST: gi|21594533|gb|BQ610182.1|BQ610182
EST:     GAAAGGTGGAACTTCAGCATTGAGACTGACTGCGAGGTTGTTGAGAAGGG                         TGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCAT
genomic: GAAAGGTGGAACTTCAGCATTGAGACTGACTGCGAGGTTGTTGAGAAGGGgtgggtaact ... aatctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCAT
EST: gi|24206284|gb|BU965537.1|BU965537
EST:     GAAAGGTGGAACTTCAGCATTGAGACTGACTGCGAGGTTGTTGAGAAGGG                         TGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCAT
genomic: GAAAGGTGGAACTTCAGCATTGAGACTGACTGCGAGGTTGTTGAGAAGGGgtgggtaact ... aatctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcccttggtttatgcttttcatttttttcatttgctttttttaatctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCATTATGAGGCAGATTGCTTCAAGTATCACTTATTTGCCATGCCTGGATGAA
                                         ttttaat  putative branch site (score: 3)
                 cttttcatttttttca  CT-rich tract
                  ttttcatttttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattcaaacagtgcctaatcccagacttaattatcttcctttaaaactcccttggtttatgcttttcatttttttcatttgctttttttaatctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCATTATGAGGCAGATTGCTTCAAGTATCACTTATTTGCCATGCCTGGATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - -cagtgcc
- - - - - - - - - - cccagac
- - - - - - - - - - - - - - - - - -cttcctt
- - - - - - - - - - - - - - - - - - - - - - - -ctccctt