Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacggcgaataaaaccagcaagcaccaaccatgttttatgttgagaatctacaatacgcatctcttttttgacgagggtttatgttgttgtttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTCGTGCTCAACATGTTCATCGTGGTGTGGGTGCTCGTGGTGGGCTTCGGGC

Basic information

species Oryza sativa
transcript LOC_Os01g63770.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G127949_T03 (Zea mays), 3'ss of exon 4
-cacggcgaataaaaccagcaagcaccaaccat--gttttatgttgagaatctacaatacgcatctcttttttgacgagggtttatgttgttgtttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTCGTGCTCAACATGTTCATCGTGGTGTGGGTGCTCGTGGTGGGCTTCGGGC
   |    | | |   |||      |   | ||   ||| ||  |||  |       |  |  | ||  |    |  |    |||| ||||| ||||||||||||||| ||||||||||| || |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| ||||||||||
tatcttttattcatgtcagtgctt-ctggcgatcgatttcattctgacgactgctgctctgtgtttccctgcaaaaaaaaaattat-ttgtt-tttgcaacagAACGCCGCGGAGAAGCCGCCCTTCTTCCTGCCGAGCTGGACGGGGATGTTCGTCCTCAACATGTTCATCGTGGTGTGGGTGCTGGTGGTCGGCTTCGGGC
















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|87039922|gb|CI194544.1|CI194544
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|29646076|gb|CB651083.1|CB651083
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|86494568|gb|CI137201.1|CI137201
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87042096|gb|CI194720.1|CI194720
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87039973|gb|CI194595.1|CI194595
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87041578|gb|CI196200.1|CI196200
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|86502680|gb|CI145313.1|CI145313
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|86479174|gb|CI121807.1|CI121807
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|86858545|gb|CI273104.1|CI273104
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87040985|gb|CI195607.1|CI195607
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|86484225|gb|CI126858.1|CI126858
EST:     CATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: CATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87038740|gb|CI192779.1|CI192779
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|88198140|gb|CI197990.1|CI197990
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|88198342|gb|CI198192.1|CI198192
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|88197295|gb|CI197145.1|CI197145
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87039397|gb|CI194019.1|CI194019
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAGGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|88198128|gb|CI197978.1|CI197978
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|88198063|gb|CI197913.1|CI197913
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87039545|gb|CI194167.1|CI194167
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87036225|gb|CI190847.1|CI190847
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAGGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87040152|gb|CI193361.1|CI193361
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
EST: gi|87038911|gb|CI193533.1|CI193533
EST:     TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATG                         AACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC
genomic: TCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 48 (upstream exon), 66 (downstream exon)
Score: 8

CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCACTCGCCCACATCCTCACCTACCGTACGGCCTCCGCGCGCATGgtaacctcaa ... tttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTCGTGCTCAACATGTTCATCGTGGTGTGGGTGCTCGTGGTGGGCTTCGGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctacaatacgcatctcttttttgacgagggtttatgttgttgtttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTCGTGCTCAACATGTTCATCGTGGTGTGGGTGCTCGTGGTGGGCTTCGGGC
                     ttttgac  putative branch site (score: 8)
                 tctttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacggcgaataaaaccagcaagcaccaaccatgttttatgttgagaatctacaatacgcatctcttttttgacgagggtttatgttgttgtttgcaacagAACGCGGCGGAGAAGCCACCGTTCTTCCTGCCGAGCTGGACGGGGATGTTCGTGCTCAACATGTTCATCGTGGTGTGGGTGCTCGTGGTGGGCTTCGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - gaataaa
- - - - - - - - -gcaagca
- - - - - - - - - - - - - - -catgttt
- - - - - - - - - - - - - - - - - - -atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttgt