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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctcacagcttatcataacatattgaatattgattttgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA

Basic information

species Glycine max
transcript GLYMA18G51810.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------------------tttctcacagctta----tcataacatattgaatattgat-tttgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
                                                                                               |||  | || |     |||       |  |||||  | | |     | ||   ||||  ||| || | |||  || ||    | ||  ||||    || |||||||||||| ||||| || ||||||||||||||||||||||||||| |  ||||| | ||||| || ||||||||||| ||||||||||| |||||||||
gtaagtggtaacttagtctgcagttttagacttacaaaaaccaaaagtttgtttgctcatttatttgcaaattctgttggaaaatatggtctggactcttaactcaagaaccattgggctctctatattcttctctcctcgttttgcttatgc-tttgctatctagcattaaaaacatatatgtttgcttattacagTGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTTGCAAGTTCACTGGAAGCATTTGGAGGGGGGCATAATGATCCAATCAGTGTTGCTTTTGGA

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 2
tttctcacagctta-tcataacatattgaatattgattttgaagatgttagatatgtattttctttatagactttaattgctttacct-ttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
  |  ||   |    | |||    |    ||||| | |  | || | |  |  |  |   | || |  ||     | ||  ||||| | |     ||| ||| |||||| | || || || ||||||||||||||||||||||||||  |  | ||||| ||||| || || || |||||||| || ||||| |||||||| 
cattgcattacacgcttatatttaaacccatatttactc-gtagttttctgccaacttgctgctatccaggacaca-ttaatttacatatcccttttttcagGGAAGGATTAGGAGAAGCTTATGATGGAGATATTGCATTTGCAAGCTCACTCGAAACATTTGGGGGAGGCCACAATGACCCTATAAGTGTTGCTTTTGGT

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
-------------------------------tttctcacagcttatcataacatattgaatattgattt-tgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
                               |||     | |  | | | | |  |       |||||| |||| |  ||  ||      ||||| |||    ||  | |  | ||| |||||    | ||| |||||||| ||||| || |||||||||||||||||||| |||||  |  | ||||| ||||| || ||||||||||| |||||||||||  | ||||||
gtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaat-ttctacttttgt----ttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 2
-tttctcacagcttatcata-acatattgaatat-tgattttgaagatgttagatatgtat-tttctttatagacttta-attgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
 |   | ||     ||     |   ||| | | | | ||   ||  ||| | ||  ||||  |  ||   |   |  ||   || | | || || |  ||  |||||||||||| ||||| || || |||||||||||||||||||| ||  |  | ||||| ||||| || || || ||||| ||||| ||||| |||||||| 
gtaagtaaccatccattgcccatgcatttattttgtaatccggagtatggttgagctgtaagtcactccctgcgccatatgctgatatgcccttttgttt--cagTGAAGGACTAGGGGAAGCATACGATGGAGATATTGCATTTGCCAGCTCACTTGAAACATTTGGAGGAGGCCACAATGATCCAATGAGTGTCGCTTTTGGT

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------tttctcacagcttatcataac----atattgaatattgattttgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
               || |||||||| || |  |         |  || | || |||     ||   || |  | | |  ||||   ||    || | ||   |||| |  ||| |||||||||||| || ||||| || ||||| || ||||| || ||||||||  | ||||| |||||||| || |||||||| ||||| |||||||||||||||
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatctttta---acagcgatagattattctttct-ttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 2
tttctcacagcttatcataacatattgaatattgattttgaagatgttag-atat-gtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
 || | |     | |       | ||    ||  | |    |  | ||   | || | ||  |  | || |  || |||||  |    | | |   || ||||||||| |||||||| |  |||||||| || ||||| |||||||||||  | |||||||||||||| || || ||||| || || |||||||||||||||
-ttgttattcagttttggtgtttcttatggatgaaatcaacatttctttccacatagcatgcttgtcat-ggtttcaattgtctctgttctctgaattgcagTGAAGGGCTTGGGGAAGGATATGATGGGGACATTGCTTTTGCAAGTGCTCTAGAAACTTTTGGTGGAGGACACAATGATCCTATTAGTGTGGCTTTTGGA

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24732 (Selaginella moellendorffii), 3'ss of exon 2
tttctcacagcttatcataacatattgaatattgattttgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
                          | |     | |||   ||      |  ||| ||   | |  |  |     ||  |||  |||| |    | |||||||||||| || || || || ||||||||||| || ||||| ||||| |||||||| |||||||| |||||| |||| || || || || ||| |||||
--------------------------gtaagcccactttaccga----gtaattgtgttccatgttcaatccggtctttgtttctctttttttcctacagTGAAGGACTCGGTGAAGCGTACGATGGAGATATCGCTTTTGCTAGTGCTTTGGAAACATTTGGTGGCGGGCATGATGATCCCATTAGCGTCGCTGTTGGA

upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ08060 (Selaginella moellendorffii), 3'ss of exon 2
tttctcacagcttatcataacatattgaatattgattttgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
                          | |     | | |   ||      |  ||| ||   | |  |  |     ||  |||  |||| |    | |||||||||||| || || || || ||||||||||| || ||||| ||||| |||||||| |||||||| |||||| |||| || || || || ||| |||||
--------------------------gtaagcccactctaccga----gtaactgtgttccatgttcaatccggtctttgtttctctttttttcctacagTGAAGGACTCGGTGAAGCGTACGATGGAGATATCGCTTTTGCCAGTGCTTTGGAAACATTTGGTGGCGGGCATGATGATCCCATTAGCGTCGCTGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
                         ctttaat  putative branch site (score: 4)
                                       cctttgtactttcc  putative PPT
     atatgtattttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctcacagcttatcataacatattgaatattgattttgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctttg