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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgttcatttcttcctacacaattggcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG

Basic information

species Glycine max
transcript GLYMA09G13840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 4
ttttgttcatttcttcctacacaattggcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtt------tataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG
   | || || |  |  ||   |||||   | |      |   |  |||||   || ||| |  |  ||     | ||   | ||| ||||      | | ||||||||||||||||||| ||||||||    |||||||| |   ||||||| || |||||||||||||| || |||||||| ||||| |||
-catatt-atctactgttatg-aattgatatctcataact---tatttttcatatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 4
ttttgttcatttctt--cctacacaattggcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG
|| ||| |||   ||   ||   | |     |  || |   | |  |  | |        | | |   | |       | |||   |  | |||  |  ||||||||||||||||||||||| || || ||||| ||||   ||||||| || |||||||| ||||||||||| ||||| ||||| |||
ttatgtgcatactttagtctgtgcgagcaaatctttgaatatatgggaatctgacaacaattgctaactgtgggtcctttatgctgtaatattttca--cagCATAAAACTATTGATAGTGTCCTGGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGTTCTGATCTAAGTGCTGCTTCTCAG

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 5
ttttgttcatttcttcctacacaattggcttgtttaggttctctggttttctggtgt--gtagatttttttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG
|| ||| |||   ||  |        |      || |  | | |||   ||||      |    |  || |   |   | |||  ||  | |||   ||||||||||||||||||| ||||| || || ||||| ||||   ||||||| || |||||||| || |||||||||||||| ||||| |||
ttatgtgcatactttagtctctgtgcgcaaatctttgaatatatgggaatctgaccacagctactaattgtgggccctttatgatttaatatttt--aacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------ttttgttcatttcttcctacac-aattggcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtttataa-acagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG
                                                 ||| | |||| |     | || | ||  ||   ||| ||||| || ||    |||   |  |   |  ||   ||||| || ||||   ||||||  |||||||||||| |||||| |||| |||||  |||| || |||||||| || ||||| |||||||| || ||  | ||    || ||| ||
gtaagtgccgtccctggttcttgattgttgacctgcatgctttgcttcctttttacattccaatacataccagttccctccattaagttct-tgtttccaaggtcgcttaaacatggtcgttttatgctgacttttgttttatactacagCATAAAACCATTGATGGTGTCCTAGCCCGAGGTGAAAAGCTGGACAGCTTAGTGGAGAAGAGCTCAGAGTTAAGCCTGGCATCGAAG

upper sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 4
ttttgttcatttcttcctacacaattg-gcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtttataa-acagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG
  | |   | |   | ||    ||||  | ||  ||   | ||    |||  |  | | |   | || ||  | ||   |||| ||| | | | | | ||||||||| |||||||||||||| || ||  |||| ||||||||||| |||||||||||||| ||||| ||||| ||  | || || |||
--tggagaactatctgctgtctaattttgtttccttttttccttctttttatttttctatctttattcttttctttgatatgtatttttctgtttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|298197641|gb|HO045120.1|HO045120
EST:     ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
genomic: ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacac ... ttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
EST: gi|192313879|gb|FK011083.1|FK011083
EST:     ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
genomic: ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacac ... ttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
EST: gi|298168934|gb|HO009864.1|HO009864
EST:     ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGAT
genomic: ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacac ... ttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGAT
EST: gi|298164125|gb|HO013770.1|HO013770
EST:     ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGAT
genomic: ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacac ... ttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGAT
EST: gi|298163467|gb|HO012200.1|HO012200
EST:     ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
genomic: ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacac ... ttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
EST: gi|192333542|gb|FK025737.1|FK025737
EST:     ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
genomic: ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacac ... ttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
EST: gi|31469010|gb|CD411038.1|CD411038
EST:     ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA
genomic: ACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacac ... ttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctggtgtgtagatttttttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG
                                    tctttctgttt  CT-rich tract
                                      tttctgtttataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgttcatttcttcctacacaattggcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA