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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

Basic information

species Glycine max
transcript GLYMA08G13110.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
gtaaagtcatttttgtgtttgtgttta-ggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
        ||     |  || |    |   |  ||| |  |   |  |   | |||  | | ||  ||  ||       |||  |     |   |      ||  | || ||||| ||||| ||  ||||||| ||||| |   | |||| |||||||||||| ||||| ||||| || ||||| ||||| |||||||| |   |  | || |
--------atcccgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcat----tttcctggttctgagagattgctttctatg-cagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttt---tttaccttatta--tgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
                               ||   |||||  |    ||||  |    |  |  | | |     || | ||   || || | || |  | | || |  | |  ||||||||||| ||  | |||||||||||    || |||||||| |||||||| |||||||| || || ||||| ||||| |||||||| |   | || || |
-------------------------------gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G423337_T03 (Zea mays), 3'ss of exon 3
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaacta-gttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT--------
                    || |       | | |  || | |  || |         | ||  |||  ||     |      | ||   ||| |   ||    | |||||| ||||||||||  | ||||||||||||   || |||||||||||||||||||||||||| ||||||||||| ||||| || ||||| |   | || || |        
--------------------gtatacgatcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccag----cctcacagcattgtattatcc--tttggcagttgtgcagTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCTCAGGCTTC

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaacta-gttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
                    || |       | | |  || | |  || |         | ||  |||  ||     |      | ||   ||| |   ||    | |||||| ||||||||||  | ||||||||||||   || |||||||||||||||||||||||||| ||||||||||| ||||| || ||||| |   | || || |
--------------------gtatacgatcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccag----cctcacagcattgtattatcc--tttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 12
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
                    || |   | ||    ||||  ||  |||  |    | || |  |     |    |  |  || | ||  |   |    || || | | |||| ||||||| || || |||||  ||||    || || |||||||||||||| || || |||||||||||||| ||||| || ||||| |  || || || |
--------------------gtatgaggctttccagtttgttt--cttgctt---ctgggatcatggttttctcaccacattgtgactgtgcgacattatctgctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTCTTCGCTCCTATCGATGAATCTTTTGCTGACGATGCACCGTTGCTACCCT

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 13
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
                           |  ||  ||  |||  ||||  ||   ||         ||  ||    |   |||   |   | | |    ||  | |   |||||||||||||||  | || ||  |||||   || || |||||||||||||| ||||| ||||| |||||||| ||||| || ||||| |  || ||||| |
---------------------------gtatggaggccttccaatctgtttcttgc---------ttcttggttcttgctttacaattgtgtgacattatcggctactgcagCTGTGCAGTGGCGTCGACGAGGATGCACCTGGTGCGTGTGCACAGCTTGTCTTTGCTCCTATTGATGAATCTTTTGCCGACGATGCACCGTTGCTGCCCT

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
                |||||  ||||   |   |    ||     || ||||||     |  ||||| ||  | ||| || ||    |  || |    ||||      ||||| || || ||  ||||||||||||   | ||||  ||||| |||||||| ||||| || ||||||||||||||||| |||||||| |  || || ||||
----------------gtttgc-tttatactaaagacactcagggattcttaaag-----atgagttattgaaattgaattcttggtttcttttttgcttttgtc----cagCTTTGTAGCGGCGTTGATGAAAATGTGGTTGGAGGTTGTGCTCAGCTTGTCTTTGCCCCAATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttgg--tgtggc--agCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
                               ||| |  ||| ||  |||       ||   |||    |  |   || | | || |    ||| || | | | |  | | |   |||| || || ||  ||||||||||||   | ||||  |||||||||||||| ||||| |||||||||||||||||||| |||||||| |  || || ||||
-------------------------------gtttgacttcatactttaactccaaagtttctatgctcctt---tgttctcttcatgacattttggattcttgattcttgtctagCTTTGTAGCGGTGTTGATGAAAATGTGGTTGGAGGTTGTGCACAGCTTGTATTTGCCCCTATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 13
gtaaagtcatttttgtgtttgtgtttaggttgttggtttt-cttatcttattaa--agcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
||    |  | | |   |   | |||| |    || |||| |||||||| || |   | || |  | || | | |   | |||    ||  |  || |  |||||  |||||||||| ||||||||  ||||||| ||||||   || || ||||| ||||| || ||||||||||| |||||||||||||| ||||||||||  || ||||| |
gttggtttgtctata-ataaatatttatgggagtgattttgcttatctttttcataggtagaactttgtaagtttatcttattgacataaatatttcttaaattttctgtggcagCTATGCAGTGGGGTTGATGAGAATGCAGCTGGTGCCTGTGCTCAGCTGGTTTTTGCACCTATTGATGAATCATTTGCTGATGATGCTCCTTTGCTGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT
                aatgatttttttacct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG