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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttttaggattaattttttttatcacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

Basic information

species Glycine max
transcript GLYMA08G04580.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
aggttttaggattaattttttttatcacagtttctccctgat-taagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
               | | |||| | ||| |      ||| | |||| |  | |||   ||    |||  | || || | || ||   |  | |  | |||| ||||| | ||| ||||||||| |  | ||  |||||||||| |||||||  ||||| ||||| ||||||||||| |||||||||||||| ||||||||
--------------gtatatttttttacaatggaaatctggtataagcttatctgtgtgcaaataaat--tctaatacttatctt---tcaatt--tacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA

upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
-----------------------------------aggttttaggattaattttttttat----cacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatg-atattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
                                     | |||||  || ||| |  | ||    || ||    | ||  | |   |||   || |||||| |   |  ||| |   || ||||| | ||      |  ||  ||||||| |   || |||||| |  | || ||||||||||| ||||| |||||||| ||||| ||||| ||||| |||||||| ||||||||||| ||
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaatt--ttgcagtgctaacatacagtttatgttcatttgtatattcattttctggct--agATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA

upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
aggttttaggattaattttttttatcacagtttc--tccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
        | ||  |||  |   | ||    ||   |    ||  ||    ||  |   ||| |  ||  |||  |  | | | |||  |   |     |||| || || | ||| || || ||| | || || ||||||||||| |||||||  ||||| || || ||||| ||||| |||||||||||||| ||||| ||
--------gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatttggcatacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA

upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 4
aggttttaggattaattttttttatcacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataat--gcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
        | ||   ||   | | | |  | | |   || |  || ||   |  |  | | |  ||| ||  ||| |  |  ||   |||  ||||   |||  || |||| |||||| || ||  |  | || ||||||||||| ||||| | ||||||||| || ||||| ||||| |||||||||||||| || |||||
--------gtatatcttaagtatgttaatggtgcaatctaa--aatttaaaagttgtataattgaatatt--actcaccaagttttcttgcctaatttccagTTGAAGTATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTA

upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
-------------------------aggttttaggattaattttttttatcacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
                         |  | ||  | ||||| | ||| ||  |  |   | |     |||  |   |       || |   | ||||  ||    | ||   |||  |  |  ||    ||| | |   || ||||   |  | || ||||||||||| ||||| || ||||| || || ||||| ||||| |||||||| ||||| |||||  |
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactca--taaaatagcactgagttatacattttttgtcatatctttctttc-ttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA

upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
--aggttttaggattaattttttttatcacagtttctccctga--ttaagttgttatgttaacattctaatgttgtac-taatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
  |  | |||    | |  | | |||| |  | |     || |  || |   ||| | | |    |   || |||  |  || | | |   |   |||  | |||| ||||||| |||||| || ||| |  | || ||||||||||| ||||| | ||||||||| || ||||| ||||| |||||||| || || || |||||
gtatatcttaactcttaagtatgttattaatggtctaatctaaaatttaaaagttgtatca----ttggatattgctcacaaagttttcttacctaatt-tccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA

upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------------------------------------aggttttaggattaattttttttatcacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
                                                       || |  |||  ||        |||  ||   || |     |   | |||| || | ||    | |||  | |  |||||||   | || |  |||||| || || |  || |||||   | |  |  | || ||||| || ||||| || ||||| ||||||||||| |||||||| || || ||||||||||||||
gtgtgttcatctgttaccggttctgttatatatccttatgcttttcagttctgttttgtgtgatctatgcgagaattcatggtacatctcgagaaataatattatattgatatcaccaagtt-catt--tgatattt--tggattcttgcagCTGACGTCTTTTCAGACATAAGACCGCTGGTTAGGTCAGTACTTGATGGGTACAATGTTTGTATATTTGCATATGGCCAGACAGGATCAGGGAAAACTTA

upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 3'ss of exon 12
aggttttaggattaattttttttatcacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgc----agCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
 | ||||     | || |||| ||     | | ||     |      | | | |  | |||| ||||| |  ||| ||  |||    ||| | ||||     ||| ||||| |  ||||||| |||| ||||  || |||| ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| || || || ||
-gtttttcatccttatattttataatttggatccttgaatagatctctttcaagaaatcattataatgcttgactcatattat--gcttggaaaatgtttgtagCTGAGGTGTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATA

upper sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S34_101V6.1 (Physcomitrella patens), 3'ss of exon 13
aggttttaggattaattttttttatcacagtttctccctg---attaagt-tgttatgttaacattctaatgttgtactaatgatattaa-attgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
     |||  ||  | | ||||| ||     | ||| |     ||  ||  | ||   ||   | ||  || || |  | ||    ||||  |||  |  | ||| |||||| |     ||||  ||  | || ||| | || ||  | ||||||| |||||| ||||| ||||||||||||||||| || || || || || ||
-----ttataatatagtatttttgtcgttcatgctctcaagaaatcgagcctcttggcttttaactcgtattttctgatgatagatttaatgttggtttgttcagAGGAGGTTTTTCTAGACACACAGCCATTGATACGGTCTGTATTGGATGGATTTAATGTATGTATCTTTGCTTATGGCCAAACGGGGTCTGGAAAGACCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA
                          tactaat  putative branch site (score: 1)
                       ttgtactaatgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttttaggattaattttttttatcacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

- - - - - - - - - - - - - - - -ttctccc
- - - - - - - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgta