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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattgcttgtagttaagaaaaatacaaaatgggaaagtaaattgttattgtggaaaattttatgcaacttggtgctaacacttgcctgttggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAAGATGTTTCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCT

Basic information

species Glycine max
transcript GLYMA15G07570.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0445g00060.t01 (Vitis vinifera), 3'ss of exon 1
--taattgcttgtagttaagaaaaatacaaaatgggaaagtaaattgt-tattgtggaaaattttatgcaacttggtgctaac--acttgcctgttggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAAGATGTTTCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCT
  |    |  | | | |   |    |    | ||     ||    | |  ||||     |   | ||   || ||| |||||   | |||   |||   || |||||||||||||| ||||||||||| | ||||||||| ||  | || ||||||||| | |||||||| |||||||| || || || ||||||||||| ||| 
attggaaggctcttgctcctatgttttagtattgaatctgttctctttgcattgccatgatgctcat---acctggggctaagcaaattggaggtt--tttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAAGATTTCTCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCC

upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 10
taattgcttgtagttaagaaaaatacaaaatgggaaagtaaattgttattgtggaaa-attttatgca-acttggtgctaac--acttgcctgttggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAAGATGTTTCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCT
  ||||   |    | |     ||     |      | |   || |  |||       ||  |   || || ||| |||||   | |||   |||   || |||||||||||||| ||||||||||| | ||||||||| ||  | || ||||||||| | |||||||| |||||||| || || || ||||||||||| ||| 
--attggaaggctcttactcctatgttttagtattgaatctgttctctttgcattgccatgatgctcatacctggggctaagcaaattggaggtt--tttgcagCAAAGCTTTTTAGAAGAGTTGGAAAAGACTGTTGCGCTGTTGGCATTTGAAGATTTCTCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCC
















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|192297765|gb|FG989971.1|FG989971
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAG
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAG
EST: gi|193499523|gb|FK461276.1|FK461276
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
EST: gi|38193470|gb|CF922676.1|CF922676
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
EST: gi|16348257|gb|BI973852.1|BI973852
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
EST: gi|58021979|gb|CX708720.1|CX708720
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
EST: gi|15812571|gb|BI784846.1|BI784846
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAGAGAACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
EST: gi|192328969|gb|FK021072.1|FK021072
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
EST: gi|208317059|gb|GE111500.1|GE111500
EST:     AAGCTCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGTTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
EST: gi|22928038|gb|BU545177.1|BU545177
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
EST: gi|151408269|gb|EV278077.1|EV278077
EST:     AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAAT                         CAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA
genomic: AAGCGCTAGAGTTTGCCCAAGAGGAGCTTGCACCAAGGGGAGAGGAAAATgtaaatctca ... tggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtggaaaattttatgcaacttggtgctaacacttgcctgttggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAAGATGTTTCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCT
                            tgctaac  putative branch site (score: 1)
         aaaattttatgcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattgcttgtagttaagaaaaatacaaaatgggaaagtaaattgttattgtggaaaattttatgcaacttggtgctaacacttgcctgttggatttcagCAAAGCTTTTTGGAAGAGTTGGAGAGGACTGTTGCACTTCTTGCCTTTGAAGATGTTTCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT