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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcctctcgagtgaagtcaggtcatggtatatatttacattcaacactggatattgtatatgatgaaataattttttaaaaatttgtattcgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGCATAGAGCCCTTAAGTTGCCAACACTGCCAAAACCCCTGGTAGGAGTAAT

Basic information

species Oryza sativa
transcript LOC_Os02g45650.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 1
-tgcctctcgagtgaagtcaggtcatggtatatatttacattcaacactggatattgtata--tgatgaaa-taattttttaaaaatttgtattcgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGCATAGAGCCCTTAAGTTGCCAACACTGCCAAAACCCCTGGTAGGAGTAAT
 |   |  |  |  | |||   |       | ||||||| |   |   ||  | |||| ||  || |   | | ||  ||| || |  |||||  || ||||||||||||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||| ||| |||||||  |||||||||||||| | ||||||||
cttgattacatgatatgtctaatttcaccgt-tatttacttggtatgttgt-tgttgtttacttggtatgactgatgcttttaaca--tgtatatgtgttgcagGCTTTATGATTTTCATGTACATATTTGAGACATATCTTGACATCCGTCAGCATAGAGCCCTCAAGCTGCCAACTTTGCCAAAACCCCTGCTGGGAGTAAT

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 1
--tgcctctcgagtgaagtcaggtcatggtatatatt-tacattcaacactggatattgtatatgatgaaataattttttaaaaatttgtattcgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGCATAGAGCCCTTAAGTTGCCAACACTGCCAAAACCCCTGGTAGGAGTAAT
  | | |     |   | |    ||||  | ||  |  ||   |      ||  || |   | |||   | |  | ||||||| |  || ||  || ||||||||||||||||||||||||  ||||||||||| ||||||||||||||||||||||| ||||| ||| |||||||  |||| ||||||||| | ||||||||
attacatgatatgcctaatgtcatcattatttacttggtattgttgttgttgtttacttggtgtgactga-tgctcttttaaaca--tgaatctgtgttgcagGCTTTATGATTCTCATGTTCATATTTGAGACGTATCTTGACATCCGTCAGCATAGGGCCCTCAAGCTGCCAACTTTGCCCAAACCCCTGCTGGGAGTAAT
















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|88392342|gb|CI612816.1|CI612816
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|88732275|gb|CI757123.1|CI757123
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|58671695|gb|CK060381.1|CK060381
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTACATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|88722297|gb|CI745807.1|CI745807
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|88737616|gb|CI761124.1|CI761124
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|88394689|gb|CI622563.1|CI622563
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|88760844|gb|CI770400.1|CI770400
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|58678385|gb|CK067072.1|CK067072
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTACATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|58678409|gb|CK067096.1|CK067096
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTACATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|58686372|gb|CK075059.1|CK075059
EST:     CGCCA-CCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTACATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|58683468|gb|CK072155.1|CK072155
EST:     TGGCGCTTCCTTAACTGGAGGGCGTGCTGT                         GCTTTATGATTCTCATGTACATATTTGAGACATATCTTGACATCCGTCAGC
genomic: TGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|58664452|gb|CK053138.1|CK053138
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTACATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|88824982|gb|CI775547.1|CI775547
EST:     CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC
EST: gi|58657010|gb|CK045690.1|CK045690
EST:     CGCCA-CCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGT                         GCTTTATGATTCTCATGTACATATTTGAGACATATCTTGACATCCGTCAGC
genomic: CGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGC

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: 65 (upstream exon), 71 (downstream exon)
Score: 12

CCTCCTCTCCCCCGTCTCCCGCCGCCTAGCGATTCCCGGAGCGCCTCCTCCGCCACCCATCCTGCTCCAATGGCGCTTCCTTACCTGGAGGCCGTGCTGTgtaagatttc ... cgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGCATAGAGCCCTTAAGTTGCCAACACTGCCAAAACCCCTGGTAGGAGTAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggatattgtatatgatgaaataattttttaaaaatttgtattcgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGCATAGAGCCCTTAAGTTGCCAACACTGCCAAAACCCCTGGTAGGAGTAAT
                                           ttcgtttt  CT-rich tract
     atattgtatatgatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcctctcgagtgaagtcaggtcatggtatatatttacattcaacactggatattgtatatgatgaaataattttttaaaaatttgtattcgttttgcagGCTTTATGATTCTCATGTATATATTTGAGACATATCTTGACATCCGTCAGCATAGAGCCCTTAAGTTGCCAACACTGCCAAAACCCCTGGTAGGAGTAAT

tgcctct
- - - - - - - - - - - - - - - - - - -cattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgaa