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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT

Basic information

species Glycine max
transcript GLYMA14G06340.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 23
----ctgcacctccgtcactttagaggagctatatttgtgatcctt--aatacaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
        |      | | | |  |     | || || |  | |||   |  |   ||||| || |   || ||    |    | |     || |||   || ||| ||||| ||||| ||||||||||||||| |||||| |||||||||  | ||||| |||||||||||||||||||| ||||| || || || ||||| |||
gtatgcaaattgtttttattcttcataccttttaattttatttcttctgaatctttaaatccatcta--ttgattgcttacatagaaatcgat-ttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaatt--ttctttaatacaatgttcacatg---cttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
  | |      |   |||  |      ||| || | ||  |   |   |  ||||  |   | | |  ||  | || | ||||     |    |||   || ||| ||||| ||||| ||||||||||||||| |||||| |||||||||  | ||||| |||||||||||||||||||| ||||| || || || ||||| |||
--gtatgcaaattgttttt-attcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 21
------------ctgcacctccgtcactttagaggagctatatttgt---gatccttaatacaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
             |      | || |||   || |   | | |||||     ||||  ||| |   |   |    ||  |    || ||| |||||   |   ||   ||  ||||||||| ||||||||||||||||||||| |||||| |||||||||| | ||||| |||||||||||||||||||| ||||| || || || || || || 
gtatataattatttttgttcctgttact---gatgccttttgtttgttccagtcctctatatattgagcaatggctcgcttggtca-tgt-cacataaat---ttaaaatttcagATATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACCGCA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 12
ctgcacctccgtcactttagaggagctatatttgtgatccttaataca------ccaaatcaattttct--ttaatacaatgttcacat-gcttatatt-gtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
       |     | |||  |        | ||||||  | |  | ||      ||| ||||||| |||    | |   ||||||| || || | ||||    ||||||| ||||| ||||||||||||||||||||| |||||| |||||||||| | || || |||||||||||||||||||| ||||| || || || || ||||| 
----gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
ctgcacctccgtcactttagaggagctatatttgtgatccttaataca------ccaaatcaattttct--ttaatacaatgttcacat-gcttatatt-gtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
       |     | |||  |        | ||||||  | |  | ||      ||| ||||||| |||    | |   ||||||| || || | ||||    ||||||| ||||| ||||||||||||||||||||| | |||| |||||||||| | || || |||||||||||||||||||| ||||| || || || || ||||| 
----gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 23
ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
       |   | | | | |   | ||| | || | |      |||  ||| |  | ||   ||  | || |  | |||| |   || ||   |   ||| || || || ||||| |||||||||||  | ||||  || ||||||      || ||||||||||| ||||||||||| || || ||||| |||||||||
------gtatttgattattgctta-ctagacttcttactt---atattccacactagttactttgtagactacttacacacg---attttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
 |       | | ||||  ||  |    |  |||| |  ||     ||| |     | |||      ||   |||| | |  |   | ||   ||   || ||||| || ||||| |||||||||||| |||||| ||| ||||| |||    | ||||| |||||||| || |||||||| || ||||| |||||||||
gtattttatcattacttacgaaaa----ttcttgttactct-----cacaatggtgacttt-----gtagtttgttaatacacaagtttt-caattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 23
ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaatt--ttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
       |  || ||||        |   || | | ||| |  || ||   | ||| ||  | | |  |  | |  | ||||| |||  |||       ||||||||| ||||| || ||||||  |||| | ||||  ||||||||||| ||||||||||| |||||||| || || |||||||| || ||||||||||||
------gtttgtgacttgtttacttcccgatatattatcat--atgcatggattcatttggtacatggacgctacttacacatacttccattt------cagATATGTAGTTGAAAGGATGGATTCTGATCTCTGGGAGAAAGTTCTTGACCCTGATAATGATTATAGAAGACAGCTCATTGATCAAGTAGTATCTACTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
                ctttaat  putative branch site (score: 4)
     aaatcaattttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT

- -cacctcc
- - - - - - - - - - - - - - - - - - - - - - - caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct