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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaattcttgactctccagttgatatacttcacattcagatatttgtttgtgtcacaaaataaaattctcttaattatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTTTCCACGACAGGGATATAGCCCCTGATGGAAAAACTCTTGAG

Basic information

species Glycine max
transcript GLYMA17G07380.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
gtatgttaattcttgactctccagttgatatacttcacattcagatatt---tgtttgtgtcacaaaataaaattctcttaatt---atcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTTTCCACGACAGGGATATAGCCCCTGATGGAAAAACTCTTGAG
|||||   |||      | ||  ||| |  | |    ||||  ||  ||    |||||  | |  ||  |    | ||| ||||   ||  ||||||||||| |||||||||||||    || || || ||||||   ||||| ||||| ||||||||||| ||||||||||| ||||| ||   |
gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgttaattcttgactctccagttgatatacttcacattcagatatttgtttgtgtcacaaaataaaattctcttaattatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTTTCCACGACAGGGATATAGCCCCTGATGGAAAAACTCTTGAG
||| ||  |   |    | |   |||  | | ||   | ||      ||    ||||     |  ||    | | ||  |||   ||||||||||||||||||||||| | |  ||||| || ||||| |  |||||||| || ||||| || ||||| |||||||| |  || ||||||
gtaagtccagattgtgtttttatgttagt-ttctcttcgttatcgagtta--ctgtgatttgagttactgat-tgttgtttaatgcagTGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTTTTCATGACAGAGACATAGCACCTGATGGCACTACACTTGAG

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 6
gtatgttaattcttgactctccagttgatatacttcacattcagatatttgtttgtgtcacaaaataaaattctc-----ttaattatcac--agTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTTTCCACGACAGGGATATAGCCCCTGATGGAAAAACTCTTGAG
||| ||| | |||  | | | |  |  || || || |   |  || | | || | |  ||  |   |   || ||     |||| ||  ||  ||||||||| ||||||||||||||    || || || || ||  | ||||| ||||| ||||||||||||||||||||||| ||||| || |||
gtaagttgaatctatattgttct-tccattta-ttaattgttggaaaatagtgtataacatgaccgatctttttcctctattaaatacaacttagTGAGAGCCAACTTTGAGTTCATTGAAAAGCTTGGAGTCGATCTATGGTGCTTCCATGACAGGGATATAGCCCCTGATGGTAAAACCCTGGAG

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|208292883|gb|GE094663.1|GE094663
EST:     CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAA                         TGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
genomic: CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAAgtatgttaat ... attatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
EST: gi|19053273|gb|BM731940.1|BM731940
EST:     CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAA                         TGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
genomic: CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAAgtatgttaat ... attatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
EST: gi|163926470|gb|EH039217.1|EH039217
EST:     CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAA                         TGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
genomic: CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAAgtatgttaat ... attatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
EST: gi|24136612|gb|BU927122.1|BU927122
EST:     CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAA                         TGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
genomic: CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAAgtatgttaat ... attatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
EST: gi|192294738|gb|FG986587.1|FG986587
EST:     CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAA                         TGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
genomic: CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAAgtatgttaat ... attatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
EST: gi|213600839|gb|DB956231.1|DB956231
EST:     CTGGCCATGGGAAGATGGTACCAATTCATTAAACATGGCTAANAGACGAA                         TGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT
genomic: CTGGCTATGGGAAGATGGTACCAATTCATTAAACATGGCTAAAAGACGAAgtatgttaat ... attatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacattcagatatttgtttgtgtcacaaaataaaattctcttaattatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTTTCCACGACAGGGATATAGCCCCTGATGGAAAAACTCTTGAG
                                        tcttaat  putative branch site (score: 3)
                          acaaaataaaattctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaattcttgactctccagttgatatacttcacattcagatatttgtttgtgtcacaaaataaaattctcttaattatcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTTTCCACGACAGGGATATAGCCCCTGATGGAAAAACTCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA