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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattttttttaatgatctttgaaaactattttgtcatcccaactcttgcttgctctttttttttgaacaacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATACTGGCCTACAAATTTGGAGCTCCCTTTGCACTGATTACTTCCTTATCAGTTGCTGCTTATGTTGCTTTTACACTGACTA

Basic information

species Glycine max
transcript GLYMA14G38800.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G58270.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------gattttttttaat----gatctttgaaaactattttgtcatcccaactcttgcttgctctttttttttgaacaac-ttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATACTGGCCTACAAATTTGGAGCTCCCTTTGCACTGATTACTTCCTTATCAGTTGCTGCTTATGTTGCTTTTACACTGACTA
                                            |||||| | ||     ||  |||  |  |  |   ||||        ||   |  || ||  | |  || |||  ||  |  | |||| |||||||  | ||||||||||||||| ||||||||||||| ||||| ||||||||| | |||||   |||||||||  | || ||||   | ||| | | ||| ||| |  || 
gtaaagcttgtctgaccacttggtgctttctcatgatcattgttttttttctcattttgaataattggcagttgctcattcatatttggatttcactattcattcgtctctaaaaacactcgacgtaattaatatgtatct-ttcagATATCTATGGTATCAGGTATACTGGCATACAAGTTTGGAGCTGCTTTTGCCTGGATTACTTCTCTCTCCGTTGGATCATATATCGTTTTCACATTAGCTG

upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g08350.t01 (Vitis vinifera), 3'ss of exon 6
--gattttttttaatgatctttgaaaactattttgtcatcccaactcttgctt---gctctttttttttgaacaacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATACTGGCCTACAAATTTGGAGCTCCCTTTGCACTGATTACTTCCTTATCAGTTGCTGCTTATGTTGCTTTTACACTGACTA
   ||||  |||    |||||||     |||  || |||  | |  |||||||     ||||| | | |||| |  |||| || ||||||||  ||||| ||||||| || |||||||||||||| || || |||||||| |||||  | ||||||  ||| |||||  ||||||||||||| ||||||||||| ||| |  || 
gttatttcatttggc-atctttgg----tatgatgacatttctatccttgcttttgattctttgtctctgaatagtttcaacatatttaacacatatccttccagATTTCGATGGTAGCAGGTATTCTAGCATACAAATTCGGAGCATCTTTTGCATGGATAACTTCGCTATCAGTTGCTGCATATGTTGCTTTCACATTAGCTG

upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S209_119V6.1 (Physcomitrella patens), 3'ss of exon 8
gattttttttaatgatctttgaaaactattttgtcatcccaactcttgcttgctctttttttttgaacaacttcagcagatttaacatgtatcc--------atccagATATCTATGGTAGCAGGTATACTGGCCTACAAATTTGGAGCTCCCTTTGCACTGATTACTTCCTTATCAGTTGCTGCTTATGTTGCTTTTACACTGACTA
 | |  | | | ||    ||  ||||| |    |  ||  || |  |  |     |  || |     ||  ||||  | | ||| | || ||||         | |||||||| ||||| || || |||||||| ||||||||||||||||| ||||||  ||| || ||  |  | || |||||||||  |  ||| ||| || || 
-agtggtgtcactg----ttagaaactgt--aattgtcttaaataattttgatattggttatgaaggcagtttcaa-aaacttagcttgcatcctgctttttgtgcagATATCAATGGTGGCTGGAATACTGGCATACAAATTTGGAGCTCCATTTGCATGGATCACGTCTCTTACCGTGGCTGCTTATACTCTTTTCACATTGTCTG

upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S249_41V6.1 (Physcomitrella patens), 3'ss of exon 8
gattttttttaatgatctttgaaaactattttgtcatcccaactcttgctt-gctctttttttttgaacaacttc--agcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATACTGGCCTACAAATTTGGAGCTCCCTTTGCACTGATTACTTCCTTATCAGTTGCTGCTTATGTTGCTTTTACACTGACTA
      |  |     | || |||| |     | ||     | ||| || || | |||        |   || |||  |||  |  || |   |     | |||||||| |||||||| || ||||| ||||||||||| |||||||| |||||   ||| || ||| |  | || ||||||||   |  ||||||| ||||| 
---gagtaatggcattattagaaagcatagatttccgtaaatctcctgttttgttctggcgcagcgtcgaatttcttagcttacataccgcattctgttgcagATATCGATGGTAGCTGGGATACTAGCCTACAAATTCGGAGCTCCATTTGCGTGGATCACCTCCCTCACTGTGGCTGCTTACACTCTTTTTACATTGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttgctctttttttttgaacaacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATACTGGCCTACAAATTTGGAGCTCCCTTTGCACTGATTACTTCCTTATCAGTTGCTGCTTATGTTGCTTTTACACTGACTA
                                  atttaac  putative branch site (score: 3)
                                              tccatcc  putative PPT
          tttttttttgaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattttttttaatgatctttgaaaactattttgtcatcccaactcttgcttgctctttttttttgaacaacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATACTGGCCTACAAATTTGGAGCTCCCTTTGCACTGATTACTTCCTTATCAGTTGCTGCTTATGTTGCTTTTACACTGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - catccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcagc