Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataatggccattaagaataacagcttgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os12g44000.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 4
ctctgtgattgtgaacca-----aaagagagatgagatacagtttttatgcataaatataatggccattaagaataacagcttgctgctggt-catatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
   || ||  || ||| |        |||   |||   |      |||    | | | || |||   ||  || |||||  || |||||| | |   | ||||||||||| |||||||| || |||||||| || ||||| || || || ||||| ||||| ||  |||| |||||||| ||||| |||||||||
--atg-gaacgtaaacaatttttgtggagccttgatggatgtggattacagtttactgta-tggt--ttgtgattaacaaattcctgctgttactcttgtctgcagATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataatggccat-taagaataacagcttgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
   |   ||    || ||  |         |   || |||    | |     || | |   ||      |  | | |   ||          | | || |||||| |||||||| || ||||| || |||||||| || ||||| ||||||||||||||  | |||||| | |||||||| || | ||||
-gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 4
-ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataat----ggccattaagaataacagct-tgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
 ||     | | ||||   |   |    | |    || ||   |   |  | |  |||    ||  || ||    || |||| || || ||||    ||||   |||||| || ||||| || |||||||| |||||||| || | ||| ||||||||||||||| | || ||| | ||||||||||| ||||||
tctgaaccaatctgaaattatgcaactcttactaccatttacgacttagcagtccaatacatggttatcaaactgaaaagctgtgttgttggtt---tatc---agATATTCTATATGACTCATGGTCACCAGCAATGACAGTGAATTCAGTCTGCATCAGCATTCTTTCGATGCTATCAAGTTCACCCGCAAAG

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 4
ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataatggccattaagaataacagcttgc---tgctgg-tcatat-atctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
 | | ||  |   ||    | |  || |    ||   | | ||   |  ||  ||    || || |   | | |  ||     |  ||  |||| | || |||||||||  |||||||||||||||| || || ||||| || |||||  |||||||||||||| | || ||| | ||||| ||| | |  |||
-tttatggatccaaat---atgttagtttgattatgatgtcta-aaactaacttatgtacctttcaatctgaaattttatatttattgactcatgtgatgtgcagATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
--ctctgtgattgtgaac---caaaagagagatgagatacagtttttatgcataaatataatggccattaagaataacagcttgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
     |   ||   ||||   | |   ||  |||||  | |||  |    | | |||  ||||   |||    ||     || |    |  |  | |     |||||||| ||||||| ||||||||||| ||||||||||| || ||  |||||||||||||  | || ||||| || |||||| |||  |||
aatcatagaatgaagaacactcgacgcagtcatgagggagagtggt-gcacgttaatgaaatgatgatttttcatt----ctgggatttatttttgttcaaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
ctctgtga-ttgtgaaccaaaagagagatgagatacagtttttatgcataa-atataatggcca-ttaagaataacagcttgctgct-ggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
      || ||   |||  || || |  |        ||  ||     ||| || |   |   | |||||| |||   ||     || ||     | ||  ||||||| || ||||| ||||||||||| |||||||| || |||||  |||||||||||||  |||| |||||||| |||||| | |  |||
----acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG

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|88536811|gb|CI464600.1|CI464600
EST:     ACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: ACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|88547046|gb|CI477317.1|CI477317
EST:     CATCCACACATTTACAGCAACGGGCACATCTGTTTAN                         ATATACTGTATGATTCTTGTTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|163920049|gb|EG709843.1|EG709843
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|13896698|gb|AU183034.1|AU183034
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|8857593|gb|AU094911.1|AU094911
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|88541762|gb|CI471050.1|CI471050
EST:     GGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: GGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|88375124|gb|CI523389.1|CI523389
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|58593809|gb|CF992117.1|CF992117
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|88521140|gb|CI448799.1|CI448799
EST:     TACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: TACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|88237642|gb|CI237491.1|CI237491
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|88466336|gb|CI529745.1|CI529745
EST:     AACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: AACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|88536272|gb|CI466013.1|CI466013
EST:     CGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|8857008|gb|AU094326.1|AU094326
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|86822411|gb|CI357963.1|CI357963
EST:     GGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: GGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|5851049|gb|AU078221.1|AU078221
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|8856902|gb|AU094220.1|AU094220
EST:     CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: CCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|88549272|gb|CI479148.1|CI479148
EST:     AACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: AACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
EST: gi|86888775|gb|CI307833.1|CI307833
EST:     ATTTACAGCAACGGGCACATCTGTTTAG                         ATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA
genomic: ATTTACAGCAACGGGCACATCTGTTTAGgtaaagttgt ... atatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaatataatggccattaagaataacagcttgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
                     gaataac  putative branch site (score: 2)
                attaagaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataatggccattaagaataacagcttgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG