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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggttaataatgttgtcgccgcactctatttgtc...

Basic information

species Glycine max
transcript GLYMA15G14390.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g03060.1 (Oryza sativa), 5'ss of exon 1
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatg-aaattggagggttaataatgttgtcgccgcactctatttgtc--------------------------------
|||||||||| ||||| |||||||||||||| ||||| |||  ||||||||| |||||||| || || ||||| |||||||||||| | ||||| || ||||    || ||   ||| || |   |   |  |   |  | ||  | ||| | |   |    | || || || ||    ||| ||       | ||||||                                 
TCAAGAAGATCCGCCTGGAGCAGGAGGACGAGGGCGTCCCCTCCACCGCCATCCGCGAGATCTCGCTGCTCAAGGAGATGCAGCATCGCAACATCGTCAGgtgacccacctc-ctccctccctgctagctccatctctctctgcggctgttggttgggtgggtgggtggattgatgg-attg-cgtgatttgcgatttgtgaatgctttgggaatttggattgtgccgtgcag

upper sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 5'ss of exon 1
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggttaataatgttgtcgccgcact--ctatttgtc
|||||||||| || || ||||||||||| || ||||| |||  |||||| || |||||||| || |||||||| |||||||| ||  | ||||| || ||||      | | |   ||      ||  | ||| |      ||     ||| || | | |  ||   | ||  |    |  | |    |||   |  |||  
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGCGTCCCCTCCACCGCAATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACGGCAACATCGTCAGgtcctctctattaacactctgttgttgttaggactttggattgactaagtc-atcacgga-ctgattgattggttgcctgattgattgactgattgattgat

upper sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggttaataat--gttgtcgccgcactctatttgtc
|||||||||| || || ||||||||||| || || || |||  ||||||||| |||||||| || |||||||| |||||||| ||  | ||||| || ||||      | | |  |   |  ||     |    |  |     |||   ||  | || |          | |   |    |||   |     |  || ||  
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctctattaaccaaccctctgctgctcttgtttaggactttggattcacttattaggagtagtcatcacggactgattgattcattgattgatgtg--

upper sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G174596_T02 (Zea mays), 5'ss of exon 2
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggttaataatgttgtcgccgcactctatttgtc
|||||||||| |||||||||||||||||||| ||||| |||  ||||||||| |||||||| || |||||||| |||||||||||  | ||||| || |||||  | |  |      |     | |  | ||| ||||  |       | | ||| ||       | |        ||  || || |             
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCCTCCACCGCCATCCGCGAGATCTCCCTCCTCAAGGAGATGCAGCACCGCAACATCGTCAGgtacgt-acgttgccagtcaggttgtgttcggagtgcag-gcccccccggctatgctgctcactcacgcgctcccgtgccgt-gcag-------------

upper sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcat-ctaattccttctcctttcattggaatgca----atgtgttgttgtcgatgatgaaattggagggttaataatgttgtcgccgcactctatttgtc
|||||||||| |||||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||||||||| |||||| | ||  | ||||| || ||||        |    ||   |  | | ||||  | | |      ||  ||| |||   |        |  |||||  ||      | || ||||  |        
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattatattcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg-----

upper sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgt--------atatcatctaattcc---ttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggt-------taataatgttgtcgccgcactctatttgtc----------------------------------------------------------
|||||||||| |||||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||||||||| |||||| | ||  | ||||| || ||||         | | ||  ||   |   |     |    || | |||  ||  ||| |  ||||||   |   ||| | ||        ||| | ||    | |  || | ||||                                                             
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtt-tgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag

upper sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S25_198V6.5 (Physcomitrella patens), 5'ss of exon 3
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggt-taataatgttgtcgccgcact--ctatttgtc---
| || || || || || ||||| || || ||||| ||||| |||||||||||||| || ||||| ||||| ||||| ||||| ||| | ||||| ||| |||| |  |||| |   |  ||   ||        ||| || || |     | ||  ||  || | ||  | | ||  |  | ||   || ||  ||| |  |    
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtaca--atctcagcacgactggattttagaatttgcgatatgct----cctattttgtcatcgtagactctcatcgtactatcaaggctctgcctactcttaagc

upper sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ15022 (Selaginella moellendorffii), 5'ss of exon 2
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggttaataatgttgtcgccgcactctatttgtc
|||||||||| || || || ||||||||||| ||||| |||||||| || || ||||| || || |||||||| || ||||||||  | |||||||| ||||   |        |||   ||| |||  ||||||| | |      |     | ||    |||||   |   |                           
TCAAGAAGATCCGACTGGACCAGGAGGACGAGGGCGTCCCCAGCACGGCGATCCGCGAAATATCGCTCCTCAAGGAAATGCAGCACGGCAACATTGTGAGgtgcgtg-------tccacttccattctctggaatggatt------tctaaaacgaatcgattgggctgcccag--------------------------

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|298167421|gb|HO012684.1|HO012684
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACAATGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192301718|gb|FG994412.1|FG994412
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|298177896|gb|HO021921.1|HO021921
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|193634954|gb|FK585289.1|FK585289
EST:     CGCGGGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: CGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|9985866|gb|BE660093.1|BE660093
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|213592499|gb|DB971641.1|DB971641
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|209726535|gb|BW658089.1|BW658089
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|193656306|gb|FK603352.1|FK603352
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATT
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATT
EST: gi|298179279|gb|HO027750.1|HO027750
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTCTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|298193236|gb|HO033670.1|HO033670
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|151411049|gb|EV280860.1|EV280860
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|41145798|gb|CK606009.1|CK606009
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|193592171|gb|FK548693.1|FK548693
EST:     CCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: CCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192302862|gb|FG998544.1|FG998544
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192304397|gb|FG996719.1|FG996719
EST:     ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatc ... tggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggttaataatgttgtcgccgcactctatttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctc