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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtatttgttctttctggcaaaggcttaaattttatcaattgtttgtttcctcctccctctctgttattattattgacatttttggttgtacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTGTGAAGAAGCAACCTGTTGTGACAGAGCAGAAACTTGATCCGAGTAAATT

Basic information

species Glycine max
transcript GLYMA08G19620.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19620.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0055g00390.t01 (Vitis vinifera), 3'ss of exon 4
------gagtatttgttctttctggcaaaggcttaaattttatcaattgtttgtttcctcctccctctctgttattattattgacatttttggttgtacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTGTGAAGAAGCAACCTGTTGTGACAGAGCAGAAACTTGATCCGAGTAAATT
| | ||| | ||| | | | | | | | | || | || ||| |||||||| | |||||| | ||||||| ||||| ||||| | ||||||| ||||| | |||||||||||| ||| |||| || ||||||||||| ||||| ||||||||
aggcttctaaaaacaacttaactgcccaagaaacaga---caatagaggagagctaaaaaatttctacttaacccatctactgagttttttggtcatttg---cagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTGTGAAGAAGCAGCCTATTGTCACGGAGCAGAAACTAGATCCCAGTAAATT
















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|31307756|gb|CD392959.1|CD392959
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|192322362|gb|FK014603.1|FK014603
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|4292623|gb|AI441931.1|AI441931
EST:     TAAAGACACTGCTTAATTTCTGGGAATGAATGAGGATGATGCT-CAAATT                         ATGTTTT-CAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|192297847|gb|FG988331.1|FG988331
EST:     TAAAGACACTACTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|33387927|gb|CA851134.1|CA851134
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|58024842|gb|CX711583.1|CX711583
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|151407739|gb|EV277554.1|EV277554
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTCTGCGGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|8403794|gb|BE059361.1|BE059361
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGANGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|192294140|gb|FG986229.1|FG986229
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|208288358|gb|GE084371.1|GE084371
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|192334804|gb|FK025953.1|FK025953
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|58020870|gb|CX707612.1|CX707612
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|58020675|gb|CX707417.1|CX707417
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|254347672|gb|GR853921.1|GR853921
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|192334803|gb|FK025952.1|FK025952
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|9564042|gb|BE473551.1|BE473551
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|58017178|gb|CX703920.1|CX703920
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|298180054|gb|HO025269.1|HO025269
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG
EST: gi|192295778|gb|FG992604.1|FG992604
EST:     TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATT                         ATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTTTCAGATGCTTATTG
genomic: TAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttatt ... tacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcctcctccctctctgttattattattgacatttttggttgtacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTGTGAAGAAGCAACCTGTTGTGACAGAGCAGAAACTTGATCCGAGTAAATT
                           tattgac  putative branch site (score: 2)
 tgttattattattgac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtatttgttctttctggcaaaggcttaaattttatcaattgtttgtttcctcctccctctctgttattattattgacatttttggttgtacaatttagATGTTTTGCAGCAAGGCTGGACTGTGGACCCTGCCTCTCAGATGCTTATTGTGAAGAAGCAACCTGTTGTGACAGAGCAGAAACTTGATCCGAGTAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - -ttctggc