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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcccccccaccttgcttttccgccgccgcggccgccacccccctccctcctcatcccgttcgtcgtttcgcgttcgttattacgccgcaaatt...

Basic information

species Oryza sativa
transcript LOC_Os03g51080.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g51080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G826838_T01 (Zea mays), 5'ss of exon 2
CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctccccc-ccaccttgcttttccgccgccgcggccgc-cacccccctccctcctcatcccgttcgtcgtttcgcgttcgttattacgccgcaaatt
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||| |   |  | || |      ||   ||  |  ||  ||| ||     |   |  |  ||     | |    |||  | || | || |   ||      
CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTGCAGgtacgctcgctgcgccgctcctgcttgttgctccgtcgatcgctcattgatcgagccgcagatatgtatggctagttccgggtcatgatgatagcgtggt--

upper sequence: LOC_Os03g51080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S34_308V6.1 (Physcomitrella patens), 5'ss of exon 2
CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcccccccacctt--gcttttccgccgccgcggccgccacccccctccctcctcatcccgt-tcgtcgtttcgcgttcgttattacgccgcaaatt
 || || ||||||||||| ||||| ||||||||||||  |||  || |||||||||||||| | |||||||||||||||||  | ||||| || || |||||  |   ||    |  |||  |    ||    || | ||   |  |            |||       | | | ||| | || | ||   || |  | |   
GACGACATGGATGGAGCCAGAGTGTGACAAGCTCATCATGGCGGCCCTCAACAAGAACTACATTGACATGGACGAGTACCCGATTACCACTGAGCTTCAGgttttagccctttacctcttcagaaactcaattgcggaggttacggctgtagatttctgtcactggtcattgccattttgagtgcattgc-actctacgac--

upper sequence: LOC_Os03g51080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S10_153V6.1 (Physcomitrella patens), 5'ss of exon 3
CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcccccccaccttgcttttccgccgccgcggccgccacccccctccctcctcatcccgttcgtcgtttcgcgttcgttattacgccgcaaatt-----------------------------------------------------------------------------
 || |||||||||||||| |||||||||||||| || |||   ||  | |||||||| ||  |||||||||| ||||||||| | || || ||| | |||||     | |   |||     | |   |  |   || ||         |       |  |  | | |  ||   | |  |      |  ||  | | |||                                                                             
AACAACGTGGATGGAGCCTGAGTGCGACAAGCTGATTCAGAAATCATTGAACAAGAATTATATCGACATGGATGAGTACCCCATTACTACGGAAATTCAGgtgaaattgctttccaggacacatactcaacaa-gcagcaaaatgagacggggaagcatagacagatgctcaagt-gtatagacattctcgttgtagattctgtaaggattcaaattgtcttgaagtgttctagcatgagttttcggcctgcagctcattgatgcattttcgctcag

upper sequence: LOC_Os03g51080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S68_116V6.1 (Physcomitrella patens), 5'ss of exon 2
CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtact--cctcccccccaccttgcttttccgccgccgcggccgccacccccctccctcctcatcccgttcgtcgtttcgcgttcgttattacgccgcaaatt
 || || ||||||||||| ||||| || ||||||||   | |  |  |||||||||||||| | |||||||||||||||||  | |||||||| || ||||| |   |||     |  ||| | |     |        ||  |       |  | |  |  |  | ||   |     | ||   ||        || ||  
GACGACATGGATGGAGCCTGAGTGTGATAAGCTCATTATGTCTGCGCTCAACAAGAACTACATTGACATGGACGAGTACCCAATTACCACCGAGCTTCAGgtgcgagcctttagacatcctcggtaacgtggactttgagcatctgttgatcgtcgttatgcttgcattgcaccccaagagtgtatttagtgcttgcgaa--

upper sequence: LOC_Os03g51080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ18071 (Selaginella moellendorffii), 5'ss of exon 2
CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactc--------ctcccccccaccttgcttttccgccgccgcggccgccacccccctccctcctcatcccgttcgtcgtttcgcgttcgttattacgccgc--aaatt------------------------
|||||| ||||||||||||||||| || |||||| ||  ||||||  |||||||||| ||| |||| ||||||||||| || || ||||| || |||||||| |             |   | | | ||  ||| |     |||    |    |    |   |  |      |   |  |   |||   |||| ||    | |  |||||                        
CACCACTTGGATGGAGCCCGAGTGTGATAAGCTCGTCATGGCCTCGCTCAACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaagaaaatatctttcgagcatgactttgcatgttcgca-ttgttttcttaattggtttttcgtgtgagtggagaaacgctagcgtttttttttctcttaaattaatggttttttgttttgctcgtag

upper sequence: LOC_Os03g51080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ36644 (Selaginella moellendorffii), 5'ss of exon 2
CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcccccccaccttgcttttccgccgccgcg-gccgccacccccctccctcctcatcccgttcgtcgt-ttcgcgttcgttattacgccgcaaatt------------------------
|||||| ||||||||||||||||| ||||||||| ||  ||||||  |||||||||| ||| |||| ||||||||||| || || ||||| || |||||||| |           | ||  |      | |   ||  |    ||      |   |  |  |       |      | |||||  || || | |   |||||                        
CACCACTTGGATGGAGCCCGAGTGTGACAAGCTCGTCATGGCCTCGCTCAACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaagaaaatatctctcgagcatgactttgcatgtttgcattgttttttttaatggtttttcgtgaaacgctagcgttttttttttctct-taaattaatggttttttgttttgctcgtag

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|58690704|gb|CK079391.1|CK079391
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|88400383|gb|CI593458.1|CI593458
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCAGCGAACTCCAG                         AACTGATGTTGTGA
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGT-GTGA
EST: gi|88414709|gb|CI604067.1|CI604067
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AAC-GATGTGTGAACATGATTGGACACCTCTTGAATGC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGC
EST: gi|25798330|gb|CA754291.1|CA754291
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|58612489|gb|CK040201.1|CK040201
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|29617567|gb|CB622579.1|CB622579
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|88372387|gb|CI619717.1|CI619717
EST:     ACAAGAACTACGTGGACATGGACGAGTACCCCGTCAGCACCGAATTC-AG                         AAGCGATGTGTG
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTG
EST: gi|88360337|gb|CI612056.1|CI612056
EST:     ACAAGAACTACGTCGATATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACCGATGTGTGAACATGATTGCACACCCTCTTCAATGCTCCTCT
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACC-TCTTCAATGCTCCTCT
EST: gi|88398239|gb|CI588127.1|CI588127
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACTGATGTGTGAA
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAA
EST: gi|8336367|gb|BE040860.1|BE040860
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|88425374|gb|CI567094.1|CI567094
EST:     ATA-GAACTACGTCGACATGGACGAGTACCC-GTCACCACCGAACTC-AG                         AACCGATGTGTGAAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAAC
EST: gi|29659446|gb|CB655721.1|CB655721
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|88443538|gb|CI597005.1|CI597005
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AAC-GATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|117217697|gb|CT845092.1|CT845092
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|58687897|gb|CK076584.1|CK076584
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|88400360|gb|CI593435.1|CI593435
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACTGATGTTGTGAACATGATTTGCACACCTCTTCAAT
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGT-GTGAACATGATT-GCACACCTCTTCAAT
EST: gi|58663096|gb|CK051782.1|CK051782
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|58692856|gb|CK081543.1|CK081543
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|2309713|gb|C25868.1|C25868
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|58663799|gb|CK052485.1|CK052485
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|29613133|gb|CB618146.1|CB618146
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|58607481|gb|CK035514.1|CK035514
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|88304126|gb|CI599814.1|CI599814
EST:     ACAAGAACTAAGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|88392957|gb|CI614839.1|CI614839
EST:     AAAAGAACTAGGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|88330189|gb|CI658494.1|CI658494
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTC
EST: gi|58667690|gb|CK056376.1|CK056376
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
EST: gi|29659019|gb|CB655294.1|CB655294
EST:     ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAG                         AACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC
genomic: ACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGAC

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: 75 (upstream exon), 75 (downstream exon)
Score: 64

CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcc ... ctgtttgcagAACCGATGTGTGAACATGATTGCACACCTCTTCAATGCTCCTCTAGGGGACTCTGAAACGGCCGTCGGAGTCGGCACTGTCGGCTCGTCTGAGGCCATCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCACGTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGGCCTCCGTCAACAAGAACTACGTCGACATGGACGAGTACCCCGTCACCACCGAACTCCAGgtactcctcccccccaccttgcttttccgccgccgcggccgccacccccctccctcctcatcccgttcgtcgtttcgcgttcgttattacgccgcaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcggccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccgca