Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGCGCCGTGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatccgttctttccccccttcttcttctcgatccttcctgcccgcccgagtatgcatctgatcgactccatggtaaacattctttttcttgtct...

Basic information

species Oryza sativa
transcript LOC_Os02g58730.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 1
GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGCGCCGTGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggc---aatccgttctttccccccttcttcttctcgatccttcctgc-ccgcccgagtatgcatctgatcgactccatggtaaacattctttttcttgtct
||||||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||||||||||||||||| |||||||| |||||||| ||  |     ||   |||||| |    |    |||     ||||||  || | | ||   |  || | ||   |     | ||   | ||   ||  | ||   
GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGTGCCGTCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgagatttcttcttttctttttgagcctttct--tccttcacgcactggccctttgggcttttgccagggagta-ggagtaaatcggttcccctgct-

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 5'ss of exon 2
GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGCGCCGTGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaat--ccgttctttccccccttcttcttctcgatccttcctgcccgcccgagtatgcatctgatcgactccatggtaaacattctttttcttgtct
 |||||| | || ||||||||||||||||| || || || || || || || || |||||||||||||||||||| || |||  ||| || ||||| || ||| || |   ||| |  |       | |   |||  |||   || |       |    ||       |    ||  ||  |  || |   | ||   |   
CATGAGCACCTCCCGGTTCATCAAGTGCGTAACTGTCGGAGATGGAGCTGTCGGGAAGACCTGCATGCTCATCTCATATACCAGCAATACATTCCCTACTgtaagcgacaaccgcttgtggaatagtgcacattccggataggtcttttagcttcacaaatcttgtccagtttctgaatccttcacgtaaatcttgcgga--

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ09765 (Selaginella moellendorffii), 5'ss of exon 1
GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGCGCCGTGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatccgttctttccccccttcttcttctcgatccttcctgcccgcccgagtatgcatctgatcgactccatggtaaacattctttttcttgtct
 |||||| | ||  | || ||||||||||| ||||| || || || || ||||||||||| ||||||||||| || |||||   |||||| |||||||| ||  | | | |||| | | |   | | ||  |||   ||  |   ||  |   ||   | ||||  |  |                              
CATGAGCACTTCAAGATTTATCAAGTGCGTTACCGTCGGAGATGGTGCGGTGGGCAAGACTTGCATGCTCATTTCATACACGAGCAACACTTTCCCCACTgtgag-atttcgttttgttctttcctttttctctaactctcttgggctgg---gatcgttcatc-aacag------------------------------

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|88725691|gb|CI748950.1|CI748950
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|218483315|gb|FG958115.1|FG958115
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88362335|gb|CI608726.1|CI608726
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACCTTCAGTGCAAATGTTGTGGTCGA
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAAC-TTCAGTGCAAATGTTGTGGTCGA
EST: gi|163919913|gb|EG714915.1|EG714915
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|58593555|gb|CF991863.1|CF991863
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCGGATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88406286|gb|CI596413.1|CI596413
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|325493533|gb|JG458057.1|JG458057
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88314827|gb|CI608286.1|CI608286
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|86900291|gb|CI296334.1|CI296334
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|163929269|gb|EG711030.1|EG711030
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88410858|gb|CI578664.1|CI578664
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88368345|gb|CI577616.1|CI577616
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|58604410|gb|CK014938.1|CK014938
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAAATGTTGTGGTCGA
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAA-TGTTGTGGTCGA
EST: gi|218501655|gb|FG956603.1|FG956603
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88337442|gb|CI630739.1|CI630739
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCACATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|4714260|gb|AU058227.1|AU058227
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|32947879|gb|BP184451.1|BP184451
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|163920990|gb|EG710403.1|EG710403
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|218499440|gb|FG950955.1|FG950955
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88406839|gb|CI578367.1|CI578367
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|25802725|gb|CA758686.1|CA758686
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88363065|gb|CI616222.1|CI616222
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|58591734|gb|CF990042.1|CF990042
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTGAGGTAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88693672|gb|CI737247.1|CI737247
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88718274|gb|CI741363.1|CI741363
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|3763167|gb|AU029919.1|AU029919
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGCGCCGTGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatccgttctttccccccttcttcttctcgatccttcctgcccgcccgagtatgcatctgatcgactccatggtaaacattctttttcttgtct

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA