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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACTCTGGACAGATTGTCACATGGATTACTGATCCCATGCATGGAAACACCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtatttttctgctacagcattccatatttgctagtatcctttcctagtatgatgcaacaatccggtcaatctcacataaggaattaccctcattcc...

Basic information

species Oryza sativa
transcript LOC_Os07g42960.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g42960.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G359822_T01 (Zea mays), 5'ss of exon 4
CAACTCTGGACAGATTGTCACATGGATTACTGATCCCATGCATGGAAACA--CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtga-gtatttttctgctacagcattccatatttgctagtatcctttcctagtatgatgcaacaatccggtcaatctcacataaggaattaccctcattcc-------------
        |  || | || |    |||||    |   |  | |  |||||  ||   |||| ||    |  |   |||  | |       ||   |||   ||||| |||   |  |   |      ||| | ||       || ||   ||  | ||   ||   ||       |||  |   | ||||  ||| |||   |             
-----TCAGTGAGTTGGTGAAGCTGATTAAGATTATGAACCCTTCAAACAAACCTAGAAGGATCACCATAATTACAAGGATGGG--GGCAGAGAACATGAGGGTGAAgtagcctcatctca------tccgtgttgttcgcaatgctggactgat-tgtcacatggatt--actgatcctatgcatggaaacaccatcaaggccccttgtggcctg

upper sequence: LOC_Os07g42960.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G124225_T01 (Zea mays), 5'ss of exon 5
CAACTCTGGACAGATTGTCACATGGATTACTGATCCCATGCATGGAAACACCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtatttttctgctacagcattc-----catatttgcta--gtatcctttcctagtatgatgcaacaatccggtcaatctcacataaggaattaccctcattcc--------------------------------------------------------------------
|||  ||||||  ||||||||||||||||||||||| || |||||||||||||||||||| || ||||| ||||||||||||||||| || |||||||||||||||    |||  | |     |||     |||  |||| |  |||   |      |   |  | || | |  | ||  | | |      |   ||    ||||                                                                      
CAATGCTGGACTAATTGTCACATGGATTACTGATCCTATACATGGAAACACCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacgttccaccaggaacttcttgttcattcttgcaaaagtaaagtagttctgatcgcagaaatattttgctctttttaattccttggtatatgtacattggcaagtatgtgatattagaatatttgaagagttgccattttgatcatcatcttcatttatactttttag

upper sequence: LOC_Os07g42960.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G365160_T02 (Zea mays), 5'ss of exon 4
CAACTCTGGACAGATTGTCACATGGATTACTGATCCCATGCATGGAAACACCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtatttttctgctacagcattccatatttgctagtatcctttcctagtatg--atgcaac---aatccggtcaatctcacataaggaattaccctcattcc----
|||  |||||| |||||||||||||||||||||||| ||||||||||||||||||||||| || ||||| ||||||||||||||||| || |||||||||||||||    |||  | |  | | | | | ||       || |||  ||||||||  |||||     | |  | | ||||| |   ||    | |   |  || |    
CAATGCTGGACTGATTGTCACATGGATTACTGATCCTATGCATGGAAACACCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTTGACTCCATTCTGgtgagtcacgttccacca-ggaacttcttgttc------attcttctctagtatgcaatgcatttctattatgataaatctgaacgaatc--tcagttttgtttcggca

upper sequence: LOC_Os07g42960.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G117707_T02 (Zea mays), 5'ss of exon 4
CAACTCTGGACAGATTGTCACATGGATTACTGATCCCATGCATGGAAACACCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtatttttctgctacagcattccatatttgctagtatcctttcctagtatgatgcaacaatccggtcaatctcacataaggaattaccctcattcc--
|||  |||||   ||||||||||||||||||||||| ||||||||||||||||||||||| || ||||| |||||||||||||||||||| || ||||||||||||    |||  |    | | | | | ||  ||| |||  |    | | ||||  |     |  | |    |   |||| ||   ||     | |    
CAATGCTGGATTAATTGTCACATGGATTACTGATCCTATGCATGGAAACACCATCAAGGCCCCTTGTGGCCTGAAGACTCGTCCATTCGACTCAATTCTGgtgagtgaccttccaccg-ggaacttcttgttc-ctattatgatcaatttgaatgaacctcagttttgtttgggcattcatatggctgtattaggaatatgg

upper sequence: LOC_Os07g42960.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G22410.1 (Arabidopsis thaliana), 5'ss of exon 4
CAACTCTGGACAGATTGTCACATGGATTACTGATCCCATGCATGGAAACACCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtatttttctgctacagcattccatatttgctagtatcctttcctagtatgatgcaacaatccggtcaatc-tcacataaggaattaccctcattcc-
     ||||||||||||| || ||| | | |||||| ||||| ||||||||||| |||||||| |||||||| ||||||||||| || ||  ||||  ||||  || |||||     | |  | || | | |    | ||    ||  ||     |||      | |  |  ||| |  || | |  |  |     | | | 
ACGTGCTGGACAGATTGTGACTTGGGTCAGTGATCCAATGCACGGAAACACCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTGgtacgt-tttttaactcataaaactcta-actaatgattacaaattgttataccaatgtttaggttcttttgatcattgcaaatgatagaaataggaatact

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|86854539|gb|CI256661.1|CI256661
EST:     CCATGAAGGCTCCATGTGTTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|86498949|gb|CI141582.1|CI141582
EST:     CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|86854460|gb|CI256582.1|CI256582
EST:     TGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: TGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|87010184|gb|CI279281.1|CI279281
EST:     CAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|86504176|gb|CI146809.1|CI146809
EST:     CCATCAAGGCTCCATGTGGTTTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|88841088|gb|CI001050.1|CI001050
EST:     CGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|86502154|gb|CI144787.1|CI144787
EST:     CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTTTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|86499909|gb|CI142542.1|CI142542
EST:     CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCA-CCA
genomic: CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|86492916|gb|CI135549.1|CI135549
EST:     CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|88226857|gb|CI224842.1|CI224842
EST:     GAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: GAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|87035027|gb|CI189651.1|CI189651
EST:     CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|86513894|gb|CI156527.1|CI156527
EST:     CCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|88964674|gb|CI070020.1|CI070020
EST:     ATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: ATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
EST: gi|5003537|gb|AU068686.1|AU068686
EST:     CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTG                         GCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA
genomic: CCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtattt ... tgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACTCTGGACAGATTGTCACATGGATTACTGATCCCATGCATGGAAACACCATCAAGGCTCCATGTGGTCTGAAGACTCGTCCATTCGATTCCATTCTGgtgagtatttttctgctacagcattccatatttgctagtatcctttcctagtatgatgcaacaatccggtcaatctcacataaggaattaccctcattcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA