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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGAACTCCTTATGATAATGGAGTTTTCCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgtttagttagactgtcctatggaccatcttaacaattgttgagatagaatcatattattgttttttcctttggaattttagcttggttatctggat...

Basic information

species Glycine max
transcript GLYMA19G21400.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g45000.2 (Oryza sativa), 5'ss of exon 4
CTGGAACTCCTTATGATAATGGAGTTTTCCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgt-ttagttagactgtcctatggaccatcttaacaattgttgagatagaatcatattattgttttttcctttggaattttagcttggttatctggat
|||||||||| ||||| |||||||| ||||| |||||| | || ||||||||||| |||||||| |||||||||||||||   | |   | | |   | |  |        |    | || || |  | ||  ||| |  ||||   |  |||||   ||     ||| ||  | |   
CTGGAACTCCATATGAGAATGGAGTATTCCGTATGAAGCTATTGTTGTCTCGTGACTTCCCTCAGTCTCCTCCTAAAGgtagctatccctcaaaactttcagtaatgttcttctttagttcttcaagt-gaggcatttggttgtaagt--ctttgaccttcccttttgatttgcag---

upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g45000.3 (Oryza sativa), 5'ss of exon 3
----------------------CTGGAACTCCTTATGATAATGGAGTTTTCCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgt-ttagttagactgtcctatggaccatcttaacaattgttgagatagaatcatattattgttttttcctttggaattttagcttggttatctggat
                      |||||||||| ||||| |||||||| ||||| |||||| | || ||||||||||| |||||||| |||||||||||||||   | |   | | |   | |  |        |    | || || |  | ||  ||| |  ||||   |  |||||   ||     ||| ||  | |   
TCTGAATCTTGACTTGGTGCAGCTGGAACTCCATATGAGAATGGAGTATTCCGTATGAAGCTATTGTTGTCTCGTGACTTCCCTCAGTCTCCTCCTAAAGgtagctatccctcaaaactttcagtaatgttcttctttagttcttcaagt-gaggcatttggttgtaagt--ctttgaccttcccttttgatttgcag---

upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G895435_T01 (Zea mays), 5'ss of exon 4
CTGGAACTCCTTATGATAATGGAGTTTTCCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgtttagttagactgtcctatggaccatcttaacaattgttgagatagaat---catattattgttttttcctttggaattttagcttggttatctggat
|||||||||| ||||| |||||||| ||| | |||||| | |||||||||| |||||||||||| ||||| || ||||||   | |  |  ||   | | |     | || |     ||||||| ||  ||    ||  | |   | | ||   |     |  |  ||| | | |   |  
CTGGAACTCCATATGAGAATGGAGTGTTCAGGATGAAGCTATTATTGTCTCATGATTTCCCTCAATCTCCCCCAAAAGgtagttatcttctgagatttccaaacttcttcct-----ttgttgaaatgaaacctgcagttaaaaatatgttgactctttgtcattacttcgatttgcag--

upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G153924_T02 (Zea mays), 5'ss of exon 4
CTGGAACTCCTTATGATAATGGAGTTTTCCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgtttagttagactgtcctatggaccatcttaacaattgttgaga-tagaatcatattattgttttttcctttggaattttagcttggttatctggat
|||||||||| ||||| || ||||| ||| | |||||| | |||||||| || ||||||||||| ||||| || |||||| | ||  |  ||| |   | |     |  |||       ||  ||  |  | ||| | |  ||||   || |        ||   ||| ||  | |   
CTGGAACTCCATATGAGAACGGAGTATTCAGGATGAAGCTATTATTGTCACGCGATTTCCCTCAATCTCCCCCAAAAGgtatcttctg--agatt--tccaaaattctcctttgttgaagtgaagccttcagtcaaaattctgttgactcttc---gtccttcctttgatttgcag---

upper sequence: GLYMA19G21400.3 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0040g00460.t01 (Vitis vinifera), 5'ss of exon 5
CTGGAACTCCTTATGATAATGGAGTTTTCCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgtttagttagactgtcctatgg--accat--cttaacaattgttgagatagaatcatattattgttttttcctttggaattttagcttggttatctggat
|||| ||||| ||||| || || |||||||| ||||||||||||||||||| ||| |||||||| || |||||||||||||||||     | | ||   ||     |  ||   || | | ||| || ||   |||  | | | | | |   |  |    ||||||    || || ||    
CTGGGACTCCATATGAGAACGGTGTTTTCCGGATGAAGTTGTTATTGTCTCATGACTTCCCTCATTCCCCTCCTAAAGgtttgttggtacatattgctataaaattattatgcttttatatttggtgtgacc-aattttgtgactctataacctgtgaacatttta--caggctaactttc-

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|58019402|gb|CX706144.1|CX706144
EST:     CCGCATGAAGTTGTTATTGTCTCGTGTTTTCCCTCACTCTCCTCCTAAAG                         GGTTTTTCTTTACAAAGATTTTCCATCCAAATATTGCAACCAATGGAGAGA
genomic: CCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgtttag ... ttgtttgtagGGTTTTTCCTTACAAAGATTTTCCATCCAAATATTGCAACCAATGGAGAGA
EST: gi|58015211|gb|CX701953.1|CX701953
EST:     CCGCATGAAGTTGTTATTGTCTCGTGTTTTCCCTCACTCTCCTCCTAAAG                         GGTTTTTCCTTACAAAGATTTTCCATCCAAATATTGCAACCAATGGAGAGA
genomic: CCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgtttag ... ttgtttgtagGGTTTTTCCTTACAAAGATTTTCCATCCAAATATTGCAACCAATGGAGAGA
EST: gi|58021744|gb|CX708485.1|CX708485
EST:     CCGCATGAAGTTGTTATTGTCTCGTGATTCCCCTCACTCTCCTCCTAAAG                         GGTTTTTCCTTACAAAGATTTTCCATCCAAATATTGCAACCAATGGAGAGA
genomic: CCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgtttag ... ttgtttgtagGGTTTTTCCTTACAAAGATTTTCCATCCAAATATTGCAACCAATGGAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGAACTCCTTATGATAATGGAGTTTTCCGCATGAAGTTGTTATTGTCTCGTGATTTCCCTCACTCTCCTCCTAAAGgtttgtttagttagactgtcctatggaccatcttaacaattgttgagatagaatcatattattgttttttcctttggaattttagcttggttatctggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC