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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccggattttgtagtgtttgatatattataatggtatcattctgcctattgaaacttaagttgacaagttactgactgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA

Basic information

species Glycine max
transcript GLYMA17G34380.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 24
----------------------------------------------------------------------tgccggattttgtagtgtttgatatatta---taatggtatcattctgcctattga--aacttaa--gttgacaagttactgactgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
                                                                      | |    || |  ||   ||  | ||||     ||| || |  || | |||  | |     ||||  || ||  |       |  ||   |  | |||| |  ||||| |        ||||| ||||| || || |||||||||||  |  | || | ||| || || ||||| |||| |||||||||||||||||||||||||||
gtaatgcatctgcaaggagttttgctcaacaaatcaactcatttctctcctgccaagttcaatattaggatactatcttgtccagcaattattgtatttagtcaattgtttgtttttacctgataactgggttaatggtagagcaacactaaagcgctgtatatttgctgtc-acagTGAGCAATGTTCCCCCCAAGCTGGTTATCCTTCATATGAACCTTTCCCTTCTTGTATACGAGGATATAATGACGATGACTGAAAACCTGAGTGAGAAGTA

upper sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------------tgccggatt-ttgta-gtgtttgatatat-tataatggtatcattctgcctattgaaacttaagttgacaagttactgactgcata-agctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
                                                                                                             |  | || | ||| |  |||| |   | |   | || |   ||||  |    |   |   | |  | |  | || |       | | | | |||| | |  ||   | |      || |||||||| || || ||||| ||||| |||||| | | |||||| |||||||| ||||||||||||||                  
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGC-ACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA------------------

upper sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
tgccggattttgtagt--gtttgatatattataatggtatcattctgcctattg--aaacttaagttgacaagttactgactgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
      | |  ||| |   |||  ||  ||||||  |     |  |   |  ||  | |      |||| |   |  ||     ||     || || ||  |||| |        || || ||||| ||||| ||||||||||| ||||| || ||||| | ||| ||||| |||||||||||||| ||| |||||||||| ||
-attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatat---tcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA

upper sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G463904_T03 (Zea mays), 3'ss of exon 24
tgccggattttgtagtgtttgatatatta-----taatggtatcattctgcctattga--aacttaagttgacaagttactg-actgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
  || || ||   | | |   ||||  |      | |||  |    |  | || || |  || | |  ||   ||   ||||      |||| || |||| |   ||   ||   |   |  || ||||| ||||| || || ||||| ||||| ||  |||| ||||| ||||| |||||||||||||||||| |||| || ||   
--cctgagttcagaat-tcaaatatgctgacaacttatgtgacttgtacggctgttaattaaataatattactaatgcactgtgacagataacct-tgct-tcagCATCAAACAACATTCATCCCAAGCTTGTGATCCTCCACATGAACATGGCCCTCTATGTATATGATGATATAATGAGGATGACTGAAAACTTGAGCGAAAA---

upper sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
lower sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 24
tgccggattttgtagtgtttgatatattataatggtatcattctgcctattgaaacttaagttgacaagttactgactgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
          | || | |   |   | | ||    | |  |||  ||||    ||  |||    | | |||| |   |  ||   ||  | |     |||| | ||  ||  | || ||||| || || ||||||||||| |||||||| || || || || ||||||||||| ||||| || || || |||||||||||
---------gtctactctccaaaccactttacgaatgttcttc-acctac---aatgtaatccaata-gttaatccttaaatttcct--ggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA

upper sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 24
tgccggattttgtagtgtttgatatattataa------tggtatcattctgcctattgaaacttaagttgacaagttactgactgcataagctatgctat-tgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
        | ||||    || ||||||| | |      || ||  ||| | ||| |||||||||    |  | |  |||| |||  ||    | |||||    |||||||  | |||  | || ||||| ||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| |||||| |||||||||||||
---ttatatctgtatcccttaatatattttgaaaaatgtgttactattttcccttttgaaactt---ctctccatctactaacta-atgtagtttgctaaacaacagTTACATACTCAACACCGAAGCTGGTGATCCTTCACATGAATATGGCACTGCATGTGTACGAGGATATCATGAGAATGACGGAAAACTTGAGTGAGAAGTA

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|208138577|gb|GD935181.1|GD935181
EST:     CTCCTTTTCCTGATGGATCATTTGACAAACCAG                         TTAATTTCCT-CCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTA
genomic: CTCCTTTTCCTGATGGATCATTTGACAAACCAGgtactcatct ... ctattgacagTTAATTT-CTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTA
EST: gi|207683226|gb|GD665933.1|GD665933
EST:     TCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAG                         TTAATTTCT-CCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC
genomic: TCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAGgtactcatct ... ctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctattgaaacttaagttgacaagttactgactgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
                         tactgac  putative branch site (score: 1)
       aaacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccggattttgtagtgtttgatatattataatggtatcattctgcctattgaaacttaagttgacaagttactgactgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
tgccgga
- - - - - - - gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcataa