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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgattagattatattacacactcactgctacttcagcttctccagtgagagttattttggaattgacaattattcgttgtgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACATCACCCCTGGGGCCTTGGACAGGTGGGAGCAACGATTGAGTGATGTTTT

Basic information

species Glycine max
transcript GLYMA14G03500.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 2
gtatgtgattagattatattaca---------cactcactgctacttcagcttctccagtgag----agttattt-tggaattgacaattatt--------cgttgtgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACATCACCCCTGGGGCCTTGGACAGGTGGGAGCAACGATTGAGTGATGTTTT
||||| |||||| | |   | ||         || | |||   ||||  |    | |||  |     | || ||| |||||||   |||| ||          ||||   | ||||| |||||||||||||||||||| || || |||||||| ||  | ||  |||| || ||   |||  | ||  | |||||| |  ||||    ||| | ||
gtatg-gattagttaactattcattgatctaccagttactctcacttgtgaaaattcagataacttcaattgtttgtggaatttttaattcttacctttgtttttgtctttggcagTATGGTGCAGAAGAACTGATGAACTGGTAGATGGCCCTAACTCGTCTTACATTACACCAAAGGCACTTGATCGATGGGAGAAGAGATTAGAAGATCTCTT

upper sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149317_T01 (Zea mays), 3'ss of exon 2
gtatgtgattagattatattacacactcactgct-actt-cagcttctccagtgagagttattttggaattgacaattattcgttgtgcattgc----agTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACATCACCCCTGGGGCCTTGGACAGGTGGGAGCAACGATTGAGTGATGTTTT
|||||   |      |||| |  |   | ||| | |||| |  | || | ||   | |||  ||  |||   |||    |||  | | | ||||    ||||||||||||||||||||| ||||||||||| || || || || ||  ||||||| ||    ||  | ||| | |||||| | ||  ||   ||| | ||
gtatgatctcgatccatataaaccctgcgctgtttacttgccccatccctagctcgtgttgattctgaagcaacatacgttctctttcccttgcgcgcagTGTGGTGCAGAAGAACTGACGAGCTAGTGGACGGTCCCAACGCGTCCTACATCACGCCGACCGCTCTCGACCGCTGGGAGAAGCGGCTGGAGGATCTCTT

upper sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 3'ss of exon 2
-----gtatgtgatt-agattatattacacactcactgcta--cttcagcttctccagtgagagttattttggaattgacaattattcgttgtgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACATCACCCCTGGGGCCTTGGACAGGTGGGAGCAACGATTGAGTGATGTTTT
      |||||   | |  || | |    |||  | | |    | |     |  ||||  | | ||  || | | |||  ||| || | || |    |||||||||||||||||| || || ||||| |||||||| || ||||||||||||||  | ||   |||| | ||||| ||||| ||| | || | |||  | ||
tttagctatgtttctcatcttctgtcttccacatattacagagccttgagattgccagacaaattttcttggcagttg--aatcatgcattttcttctgcagTGTGGTGCAGAAGGACCGACGAGCTTGTGGATGGACCTAATGCTTCACACATGTCACCCAAGGCCCTTGACAGATGGGAACAAAGGTTAATTGACCTATT

upper sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
-gtatgtgattagattatattacacactcactgctacttcagcttctccagtgagagttatt-------ttggaattgacaattattcgttgtgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACATCACCCCTGGGGCCTTGGACAGGTGGGAGCAACGATTGAGTGATGTTTT
 |  | ||  |  | |  | |   || | ||||      |||  | |    | |||| | ||       |    | || |   | |  |   ||   |||||||||||||||||||||||||||||| || ||||| || ||||| || | ||| || ||    ||  ||||||| |||||| |  || ||   ||| | ||
agagtctgggt--acttcaatgtccattgactgggcgaccagagtttaggataagagattttgccatcctctccaatggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT

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|192314403|gb|FK008401.1|FK008401
EST:     CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATG                         TGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
genomic: CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATGgtatgtgatt ... tgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
EST: gi|192314402|gb|FK008400.1|FK008400
EST:     CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATG                         TGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
genomic: CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATGgtatgtgatt ... tgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
EST: gi|9259258|gb|BE347466.1|BE347466
EST:     AAAAGCAATTTGGGCAATTTATG                         TGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
genomic: AAAAGCAATTTGGGCAATTTATGgtatgtgatt ... tgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
EST: gi|19269235|gb|BM885491.1|BM885491
EST:     CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATG                         TGTGGTGCAGAAGA
genomic: CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATGgtatgtgatt ... tgcattgcagTGTGGTGCAGAAGA
EST: gi|151403755|gb|EV273565.1|EV273565
EST:     CACACAATTGATGACTGCAGAGCGCTGAAAAGCAATTTGGGCAATTCATG                         TGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
genomic: CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATGgtatgtgatt ... tgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
EST: gi|192318813|gb|FK011427.1|FK011427
EST:     CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATG                         TGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA
genomic: CACACAATTGATGACTGCAGAGCGCCGAAAAGCAATTTGGGCAATTTATGgtatgtgatt ... tgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttctccagtgagagttattttggaattgacaattattcgttgtgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACATCACCCCTGGGGCCTTGGACAGGTGGGAGCAACGATTGAGTGATGTTTT
                          aattgac  putative branch site (score: 3)
                          aattgacaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgattagattatattacacactcactgctacttcagcttctccagtgagagttattttggaattgacaattattcgttgtgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACATCACCCCTGGGGCCTTGGACAGGTGGGAGCAACGATTGAGTGATGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA