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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaatatacatctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgttcactttttttgtttgtttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA

Basic information

species Glycine max
transcript GLYMA13G31830.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
gtttgaatatacatctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgtt-cactttttttgtttgtttgca-tacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------
          | || |   | || ||| ||        |   |   |   || ||  |  |   |   | | ||||    ||    |||   ||||| | | ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |  ||||| ||  | || ||  ||||  | ||    |||             
-----ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG

upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------------gtttgaatatacatctc-----aatttttt--tggaaagtggaaacacttagcactttgactgaacataaccaa--agtacatgttcactttttttgtttgtttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------
                                                                                      | |  | |||  | ||     | | || |  |  |||  ||| | | |  |   ||       | ||   |||  |||  || |   |  ||||    | | || || |||||||| || ||||||||||| || ||||| || ||||||||||||||||  || ||  | || || ||  || |||| ||    | |             
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAATTATCAGAAAAGA

upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
-gtttgaatata-catctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgttcactttttttgtttgtttg-catacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------
 | || || ||| |||    ||| ||    | | |  || |  ||    ||| | |  |   | |    ||  ||||  ||  ||  ||| |   |   ||| ||||||||||| |||||||||||||| ||||| || || || |||||||| |  ||||| ||| | || ||  ||||  | |||   |||             
aggttcaacatagcatggacattcttacatacatttcaatcgttt----cttagtcaaattttcattttagatcatgacca--ttgattgctcactcaacatgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATGAAACATGCCTT

upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gtttgaatatacatctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgttcactttttttgtttgtttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------
               ||| |||| |     |         || |      |||   ||| | |       | |  |   |  ||||||   |   || | |||||||| || |||||||||||||| ||||| |||||||| ||||||||||  || ||  | || || ||| |||| || |||   | |             
--------------gtcagttttct--attatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttg---gaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA

upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------gtttg-aatatacatctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgttcactttttttgttt---gtttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------
                                                           || | || ||     |    | |  || |   |     | |||     ||  | |   |   |  | ||    | |    | || |||||      |||  | ||||||||||| |||||||||||||| ||||| || ||||| ||||||||||  ||||| ||  | || ||  |||||  |||    |||             
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgttt-cagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG

upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
gtttgaatatacatctcaatttttttggaaagtggaaacacttagcactttgactga--acataaccaaagta---catgttcactttttttgtttgtttgcata-----cagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------
||   | |   | |  | |||  |    |    |||||   |    || |   || |    || |   | | |   | |||||||| ||| ||||  ||  | |      ||||||||||||||||||||||| |||||||| || || |||||||||||||  || || |||||||||||  |||||||||||   | |             
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgactgaacataaccaaagtacatgttcactttttttgtttgtttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA
         acataac  putative branch site (score: 3)
                               ctttttttgtttgttt  putative PPT
                                tttttttgtttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaatatacatctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgttcactttttttgtttgtttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG