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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcaaaagtaccactgttaagtggtaaaatttaaaaagccgtttcagtaaacaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT

Basic information

species Glycine max
transcript GLYMA05G26230.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
aagcaaaagtaccactgttaagtggtaaaatttaaaaagccgtttc---agtaaacaattctcaaaaagttgttctaaaacatctgtttt-----tacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT
         |     | |   |   |    |||   | | | ||||    |||| || | |     || ||  ||| |   || |||         |  |  ||||||||||||||| ||||| |||||| |||| |||||||| ||  |||||||  | ||||||||||| |||||||||||||| || || |  ||||| ||||| 
--------cttttgatttattggactgcctttttgtatgtcttttccttggtaaccattccatgtcaaatttatctcattgatttgtggagtggaaatctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA

upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
-----aagcaaaagtaccactgttaagtggtaaaatttaaaaagccgtttcagtaaacaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT
     |   |   |     || ||    |  |     |    | || || ||    | | || |     |  |  ||| |  ||| |||    || |  ||||||||||||||| ||||| |||||| |||| |||||||| ||  || | ||  | ||||||||||| |||||||||||||| || || |  ||||| ||||| 
ttttgagttattggagtgccttttgtacgcgatttccttggtaaccattccatgccaaatttgt-----acctaatctcattcatttgtggaaacctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA

upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G06430.1 (Arabidopsis thaliana), 3'ss of exon 3
aagcaaaagtaccactgttaagtggtaaaatttaaaaagccgtttcagtaaacaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT
                  |||||   | |||   |  ||  | |   ||      || ||||||   |    | ||   |   || || | | |||||||||| |||||||| || ||||||||||| |||||||| ||  |  | || || || || ||| | ||||| || |||||||||||    ||||| ||||||
-----------------gtaagt--cagaatcagattagatgat---gtgtgtg-ttatcaaaagcctaaatttaa--gttcattgtt-cgttcttgcagAACATTGACTCCAGGGCATGATGCTGTTCAAAAGGTCACGTTGATACCACGAGGCCAGGCTAGAGGTCTGACTTGGTTCATTCCCTCAGATGACCCAACT

upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 3
aagcaaaagtaccactgttaagtggtaaa-atttaaaaagcc-gtttcagtaa-acaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT
                  ||||||  ||| || | ||||||| || |   ||  |  | | ||||||| ||  | ||||         |||  ||  || |||||| |||||||| || |||||||||||||||||||||||  |  | ||  | || |||||  | ||||| || |||||||||||    ||||| || || 
-----------------gtaagtgagaaacatattaaaagcctgtctgtatattattactatcaaaaacttactttaaagttataaactttggttttttacagAACATTGACTCCAGGACATGATGCTGTGCAAAAGGTAACGTTGATACCAAGAGGCCAAGCAAGAGGTCTGACTTGGTTCATTCCATCAGATGACCCGACA

upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 3'ss of exon 3
aagcaaaagtaccac-tgttaagtgg-taaaatttaaaaagccgttt-cagtaaa--caattctcaaaaagttgttctaaaacatctgttt---ttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT
           |||  ||||   ||  || |||   |    | |||| ||   ||    ||| ||||| |  | |   ||  | | | |||   |   || |||||||||||||||| || || || ||||| || || || || || ||  | |||||||||||||| ||||||||||||||||||||||||  |||||| || || 
-------ttctccatgtgttttatgcctataatcatatgtacagtttacaactaaattcattgtcaaagaact-tatgaactcttttctttgattccttttcttgcagAACTTTGACCCCAGGACACGATGCCGTTCAGAAAGTCACCCTGATCCCTCGTGGTCAAGCACGGGGTCTTACATGGTTCATTCCTTCTGATGACCCTACC

upper sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S156_30V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------aagcaaaagtaccactgttaagtggtaaaatttaaaaagcc------gtttcagtaaacaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT
                     ||    || |    |||     |  |    | |  |||         ||| | ||  |     ||| ||   || ||  || | ||   || |   |    ||||| || ||||| || || |||||||| ||||||||||| || ||  ||||| | ||||||||||| ||||| || |||||||||||    || || || || 
gtactttttctttcaccatccaattgcaattgtacctgcagtttcattgtctctggaaaatttctaaggttacggtgcattgacctctaaggcttatt--aataaattaattgtg--tgaggtgcagGACCTTGACACCAGGCCATGATGCAGTGCAAAAGGTTACCCTGATTCCTAGGGGTCAAGCTCGTGGTCTCACCTGGTTCATTCCAGGCGAGGACCCCACC

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|193633933|gb|FK582497.1|FK582497
EST:     AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGG                         AACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG
genomic: AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatt ... ttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG
EST: gi|208057025|gb|GD855138.1|GD855138
EST:     AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGG                         AACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGCAACACTAG
genomic: AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatt ... ttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAG
EST: gi|208125969|gb|GD925997.1|GD925997
EST:     AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGG                         AACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG
genomic: AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatt ... ttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG
EST: gi|208144931|gb|GD941240.1|GD941240
EST:     AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGG                         AACTTTGACTCCTGGTCATGATGCTGTGC-AAAGGTAACACTAGTTCCTCG
genomic: AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatt ... ttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG
EST: gi|208042156|gb|GD842220.1|GD842220
EST:     AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGG                         AACTTTGACTCCTGGTCATGATGCTGTG
genomic: AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatt ... ttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTG
EST: gi|7640439|gb|AW734741.1|AW734741
EST:     AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGG                         AACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG
genomic: AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatt ... ttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG
EST: gi|193417614|gb|FK382984.1|FK382984
EST:     AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGG                         AACTTTGACTCCTGGTCATGATGCTGTGCAGAAGGTAACACTAGTTCCTCG
genomic: AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatt ... ttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG
EST: gi|193588429|gb|FK538746.1|FK538746
EST:     AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGG                         AACTTTGACTCCTGGTCATGATGCTGTGCAAAAAGTAACACTAGTTCCTCG
genomic: AAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagaaatt ... ttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtaaacaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT
                        ttctaaa  putative branch site (score: 2)
                                      tttttactt  putative PPT
                                      tttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagcaaaagtaccactgttaagtggtaaaatttaaaaagccgtttcagtaaacaattctcaaaaagttgttctaaaacatctgtttttacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
aagcaaaa
- - - - - accactg
- - - - - - - - - - - - - - - - -aaaaagcc