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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agataagggattttggctgaggggagtgcattttaggatataaaatccaataatgtcccatcttcaatcccttgttcctaatgttgcagttctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTGGCTACCCTCCTGCGGCAAACTACTTGTTTCTGGGGGATTATGTGGATAG

Basic information

species Glycine max
transcript GLYMA03G39440.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39440.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 1
agataagggattttggctgaggggagtgcattttaggata--taaaatccaataatgtcccatcttca-atcccttgttcctaatgttgcagttctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTGGCTACCCTCCTGCGGCAAACTACTTGTTTCTGGGGGATTATGTGGATAG
   | |     |||| |   || | ||||| || |       |   |||| ||  | ||     ||   |    || || ||||| ||||||  || ||||||||||||||||||| |||||||| |||||  ||||||| |||||||| ||||| | ||||||||| ||||||||| | ||||| || |||||||| ||| |
---tcacttgatttgccactggagcgtgcagttaatatcgattgttatcctatcctatcattctttggtagaatttttttctaatattgcaggccttttgcagGTGATATACATGGACAGTACCAAGACTTATTGAGGCTATTTGAATACGGTGGATTCCCTCCTGCTGCAAACTACCTCTTTCTTGGAGATTATGTAGATCG

upper sequence: GLYMA03G39440.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
agataagggattttggctgaggggagtgcattttagg-atataaaatcca-ataatgtcccatcttcaatcccttgttcctaa----tgttgcagttctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTGGCTACCCTCCTGCGGCAAACTACTTGTTTCTGGGGGATTATGTGGATAG
         |||||     |    | |  |||||| | |  ||  |   |  |  |||  | | |       || ||  || |    |||||   |     ||||||||| || ||||| |||||    ||| |  |||  ||||||||||||||||| |  || |||| ||| |||||||||||| | ||||||||||| || ||
------tttattttattctattttattttattttaagcacctactagttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacactgcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG
















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|4260343|gb|AI416839.1|AI416839
EST:     CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCG                         GGGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
genomic: CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCGgttagccacc ... tctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
EST: gi|298172558|gb|HO019598.1|HO019598
EST:     CCTCTCTCAGCCAATTCTTCTCGACCTCCGTGCTCCCATCCGCATCTGCG                         GTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
genomic: CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCGgttagccacc ... tctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
EST: gi|193672040|gb|FK616310.1|FK616310
EST:     CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCG                         GTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTT-GAATATGGTG
genomic: CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCGgttagccacc ... tctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
EST: gi|298182148|gb|HO026323.1|HO026323
EST:     CCTCTCTCAGCCAATTCTTCTCGACCTCCGTGCTCCCATCCGCATCTGCG                         GTGTTATACATGGTCAGTACCGGGACTTGCTGAGGCTTTTTGAATATGGTG
genomic: CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCGgttagccacc ... tctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
EST: gi|151394657|gb|EV264528.1|EV264528
EST:     CCTCTCTCAGCCAATTCTTCTCGACCTCCGTGCCCCCATCCGCATCTGCG                         GTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
genomic: CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCGgttagccacc ... tctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
EST: gi|20449737|gb|BQ253853.1|BQ253853
EST:     CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCG                         GTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
genomic: CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCGgttagccacc ... tctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
EST: gi|298175133|gb|HO014936.1|HO014936
EST:     CCTCTCTCAGCCAATTCTTCTCGACCTCCGTGCTCCCATCCGCATCTGCG                         GTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG
genomic: CCTCTCTCAGCCAATTCTTCTCGACCTTCGTGCTCCCATCCGCGTCTGCGgttagccacc ... tctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaataatgtcccatcttcaatcccttgttcctaatgttgcagttctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTGGCTACCCTCCTGCGGCAAACTACTTGTTTCTGGGGGATTATGTGGATAG
                              tcctaat  putative branch site (score: 2)
                                            ttctcttgc  putative PPT
                                 taatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agataagggattttggctgaggggagtgcattttaggatataaaatccaataatgtcccatcttcaatcccttgttcctaatgttgcagttctcttgcagGTGATATACATGGTCAGTACCAGGACTTGCTGAGGCTTTTTGAATATGGTGGCTACCCTCCTGCGGCAAACTACTTGTTTCTGGGGGATTATGTGGATAG

- - - - - - -tggctga
- - - - - - - - - - -gggagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca