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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttatatcttattctatgatattgtgcctataatttatgtagggatgcttatttgtttcatgatcatttgtctaactataggaattttttgaagt...

Basic information

species Glycine max
transcript GLYMA18G05730.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 5
GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgt----ttatatcttattctatgatattgtgcctataatt-tatgtagggatgcttatttgtttcatgatcatttg--tctaactataggaattttttgaagt
 || || || || ||||||||||||||||||||||| ||  | || |||||||||||  | || || ||||| ||||||||||| ||  ||    ||  || ||  ||| | |||||    |||| ||   ||      ||    || ||  |    | || | |    |||||| |||| |          
-GTCTGTACTGCTAAAATGAACTTGAGTGATGAGGTTGATTTGGAAGATTATGTTTCCAGACCAGATAAAATTAGTGCTGCTGATgtgagtatcattccattttgatct-tcatattacatctatcataacataataatatatcaatctgcatttgtaccactagagcataactagaggattgccg------

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G090904_T01 (Zea mays), 5'ss of exon 5
GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttatatcttattctatgatattgtgcctataatttatgtagg---gatgcttatttgtttcatgatcatttgtctaactataggaattttttgaagt
 |||||||| |||||||||||| |||| |||||||| ||  | || |||||||||||  | || || || |||||||||||||| ||  || | | | | ||||||   | ||      |||||  |  ||     ||   | || |  |  |  |  || |  |     ||   | ||      |  
-GTTTGCACTGCCAAAATGAACCTGAGCGATGAGGTTGATTTGGAAGATTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctct-tttcattctaacgttttaaattaataatacaaatacacttgaaattcatctactggaatacaatgttgcgtctgatgccacttccgccca--

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 5'ss of exon 5
GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttatatcttattctatg---atattgtgcctataatttatgtagggatgcttatttgtttcatgatcatttgt-ctaactataggaattttttgaagt
 |||||||| || || |||||||| || |||||||| ||| | ||||| ||||||||||| || || ||||| ||||||||||||||| | ||||    |||  |||    | | | | | | |  | |  ||    |   | |  |||   |  |  | || |  | |||   |||| ||||      
-GTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTATGTTTCTCGGCCAGATAAAATTAGTGCTGCTGAGgttagcttattctgtatcttatctttacagttttcttgttgtctgagtcctcaatttcaaatgtagtactagaacttatgttcactgggggaaattttgt----

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 5'ss of exon 5
GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat--atcttattctatgatattgtgcc-tataatttatgtagggatgcttatttgtttcatgatcatttgtctaactataggaattttttgaagt---
 || || ||||| || |||||||| ||||| || || || ||||| |||||||||||| | |||||||| || |||||||| |||||  | || |  | ||   |    | | |||| |    ||  |||| | |  ||| | | |||      |   | |||| |   |||    |   ||| | ||   
-GTATGTACAGCAAAGATGAACTTAAGTGAGGAAGTTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAGgtgcgcttcttcacctccataatcggtcttgttctgcgtatgttatatggtcatgttgaattg------ggatacttgtattcttatcaacagccttttaggttac

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|6454816|gb|AW185499.1|AW185499
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|58022279|gb|CX709020.1|CX709020
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|208243697|gb|GE036996.1|GE036996
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|7146493|gb|AW508415.1|AW508415
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|18041397|gb|BM309691.1|BM309691
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGAGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|192313767|gb|FK007639.1|FK007639
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|6848666|gb|AW350956.1|AW350956
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|31461525|gb|CD403553.1|CD403553
EST:     GTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: GTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|192312053|gb|FK003844.1|FK003844
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|4396236|gb|AI495233.1|AI495233
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|192313766|gb|FK007638.1|FK007638
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|16342518|gb|BI968113.1|BI968113
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|17401263|gb|BM178045.1|BM178045
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|208106009|gb|GD904222.1|GD904222
EST:     TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG                         ATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttat ... gtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAGgtttgtttatatcttattctatgatattgtgcctataatttatgtagggatgcttatttgtttcatgatcatttgtctaactataggaattttttgaagt

- - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT