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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatctgtttacgtatttttcaatattatattttgttcaaaaattgattcacattactccttgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA

Basic information

species Glycine max
transcript GLYMA08G44580.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 4
-tatatctgtttacgtatttttcaatattatattttgttcaaaaattgattcacattactccttg-tggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
   | | |||  |   ||   |  ||  || || |   |  | | ||       ||  |||| || ||  |  | |     ||   || |   ||     ||||||||||||| |||||||||||||||||||| ||  | || ||||| || ||||||||||| ||||| || || ||||| | ||| ||  ||||||| |
aattctttgtagaaaaatagctgtatgatagatgtcagtgcagattttgcctttat--ctccgtgctgcctcatgttcttaatattctccctgctcttacagGTATTTGATTTGTTTGACACAAAACACAATGGAATTTTAGGATTTGATGAATTTGCTCGTGCACTCTCAGTATTTCATCCAAGTGCTCCACTTGATGAGA

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 4
-------tatatctgtttacgtatttttcaatattatattttgttcaaaaattgattcacattactccttgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
         || |||   |   ||| |  |   ||  || ||| |      ||| ||     || |    ||   |  | || |  ||    |  | || |   |||||||||||||||||||||||||| |||| ||| ||  |||| |||||||| ||||||||||||||||| || || ||||||||||| ||| ||||||| |
tagaaaaattagctgcacaaaaattgtggatccttg-atcttgctt-----ttggttactgata-taaaagtatatcatgtccctaatattttcttgtccattgtagGTATTTGATTTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
tatatctgtttacgtatttttcaatattatattttg---ttcaaaaattgattcacattact--ccttgtggttggtatctcatatgaacttctc-tctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
      |||  |   |||          | ||| ||     |  |  ||| ||    |||||    |    ||    || ||      | | ||  ||      ||||||||||||| ||||||||||| |||||||| ||  | || |||||||| ||||||||||||||||| || || ||||||||||| ||| ||||||| |
------tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggttactgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
tatatctgtttacgtatttttcaatattatattttgttcaaaaattgattcacattactccttgtggt-tggtatctcatatgaac-ttctctctaactt---agGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
  | ||   | |   ||  |  | |   | ||  |||  |    |   |||     | |   | ||   | ||||  | ||| | | || ||  |    |   |||||||||| |||||||| ||||||||||||||||| || || |||||||| |||||||| || ||||| || || ||||| ||||| ||| | ||||| |
--tgtccaatgaaaaatagtcaagtg--agatcctgtggatgcttactttctttccagttagtatgacattgtattgc-tataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
tatatctgtttacgtatttttcaat-attatattttgttcaaaaattgattcacattactccttgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
      | | | | | ||||| ||| |  | | ||||||    |     ||  ||  |  | || ||   | || ||     | ||   || |      ||||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||||| ||||||||||| || || ||||| ||||| ||||| || || |
-----gtatgttcttcttttttaatcaaaagactttgtt----atccatttgccaagatcctttttgaaagataacttgacagtaccaatcac------agGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
tatatctgtt-tacgtatttttcaatattatattttgttcaaaaattgattcacattactcct---tgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
       ||  |   | ||| |  | ||||||  | ||||  |||   |||    | |        | | |  |  ||     |  |  |  | |      ||||| || ||||| ||||| ||||| |||||||| |||||||| ||||| || |||||||||||||||||||| || || || ||||| || || ||||| |
-------gtaatgtttctttcttcacattataagt-gttcttaaacccatttttgtcaagatcaagtttagaagaaatgctgaaatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
tatatctgtttacgtatttttcaat-attatattttgttcaaaaattgattcacattactccttgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
      | | | | | ||||| ||| |  | | ||||||    |     ||  ||  |  | || ||   | || ||     | ||   || |      ||||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||||| ||||||||||| || || ||||| ||||| |            
-----gtatgttcttcttttttaatcaaaagactttgtt----atccatttgccaagatcctttttgaaagataacttgacagTACCAATCAC------AGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 3
tatatctgt-ttacgtatttttcaatattatattttgttcaaaaattgattcacattactccttgtggttggtatctcatatgaacttctctctaact-tagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
 |    ||  | |   | ||   | | | ||    | ||     |    |||  |      ||  |  |||  ||   ||||| | | ||    || | ||||||||||| || ||||||||||| || || || ||||| || ||||| ||||||||||||||||| || ||||| || || || || || || || || |
aactcttgcatcattgaattggtagtttcattggatatttttggaagagttccaaaagacgctcat--ttgccattgtatatgtaatgctaatcaattgtagGTATTTGACTTGTTTGACACAAAGCATAACGGAATACTTGGCTTTGAGGAGTTTGCTCGTGCTCTATCTGTTTTTCACCCCAACGCACCTATCGACGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattcacattactccttgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
                                            ctctaac  putative branch site (score: 2)
                                       cttctctctaactt  CT-rich tract
                                atatgaa  TA-rich tract