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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatattatggcaaatgtctcttcattgggctcagagtaatctaatgggaaacatatttcccaccaacatttgtgtctatatataacatatctaca...

Basic information

species Oryza sativa
transcript LOC_Os02g53060.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 5
GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatattatggcaaatgtctcttcattgggctcagagtaatctaatgggaaacatatttcccaccaacatttgtgtctatatataacatatctaca--
||||||||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||||||||| ||  ||| ||||||||||||||| ||||||||| || ||      || ||  | |  ||    ||     | |   ||   ||    | |||| |  | | | |  |     | ||| | | | | |   
GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtata-attttgcccataaagttgcattgttcctttctttcaagtagtatttcaatgccacttcc-attatcctcttggctgtaacatatcttttgtgctct

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G152775_T03 (Zea mays), 5'ss of exon 3
GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatattatggcaaatgtctcttcattgggctcagagtaatctaatgggaaacatatt-tcccaccaacatttgtgt-ctatatataacatatctaca-----
||||||||||||||||| |||||||| || || |||||||||||||||||||||||||| ||||||||||| ||  ||| ||||||||||||||| |||||||||  |||| || |     || | || ||    |||  ||| |  ||||  |     ||| | |      |  |    | |  | | |  | |  |||       
GCTGGCATGATTGTTGGAGGATGGGACAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattattttgcc-----tcccctctttcaagtca--gtatttaaatgctacttccattattctctttgctgtgacataccttctgtgccctggctagtgatct

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G152775_T01 (Zea mays), 5'ss of exon 4
GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatattatggcaaatgtctcttcattggg-------------ctcagagtaatct----aatgggaaacatatttcccaccaacatttgtg-tcta-tatataacatatctaca----------
                              || |||||||||||||||||||||||||| ||||||||||| ||  ||| ||||||||||||||| |||||||||  |||| || |     ||| |  | |  |             ||   | || |||      || || | |  ||     ||     | ||| |||| ||  |||   || |||           
-----------------------------GTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGGTATAATTATTTTGCCTCCCCTCTTTCAAgtcagtatttaaatgctacttccattattctctttgctgtgacataccttctgtgccctggctagtgatctagtaattaaatcatttactgtttgagttg

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA04G08200.1 (Glycine max), 5'ss of exon 5
GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatattatggcaaatgtctcttcattgggctcag--agtaatctaatgggaaacatatttcccaccaacatttgtgtctatatata-acatatctaca
 | ||  | |||||||||||||||||||||||||| || || |||||||    ||| || || |||||||||||  |    ||||| ||||| ||||||||||| |  | | |   |||||| |     |     |     | || | |    | |  ||| ||   |   ||||| || || |   |||| |||||| |   
ACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGTGGACAAATTTATGGAGTTCCTCTGGGTGGAACAATAGTACAACAACCTTTTGCTATCGGAGgtattt-cactgttaaaaatgtgttgaagtacaattttattattattatttctgtattcatgttcagc-taaacatgtgagtatccctatatacatatattt-

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|86496862|gb|CI139495.1|CI139495
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|2797950|gb|AA751244.1|AA751244
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTT-CAAT-GGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|8527814|gb|AU092629.1|AU092629
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|58588610|gb|CF986918.1|CF986918
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGA
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGA
EST: gi|88961062|gb|CI096465.1|CI096465
EST:     GGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTNACCTCTATGGATTGCTNGACCACGAATGGAAGGAGG
genomic: GGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|218488196|gb|FG970072.1|FG970072
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|58692319|gb|CK081006.1|CK081006
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|25799545|gb|CA755506.1|CA755506
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|87028372|gb|CI263714.1|CI263714
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|218498714|gb|FG963991.1|FG963991
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|88974504|gb|CI022045.1|CI022045
EST:     CTCAGTCCCTCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|218498950|gb|FG948071.1|FG948071
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|38472737|gb|CF956869.1|CF956869
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAACGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|88965355|gb|CI011606.1|CI011606
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|88829940|gb|CI004978.1|CI004978
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|88242742|gb|CI242591.1|CI242591
EST:     CCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|218504275|gb|FG947024.1|FG947024
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|86491932|gb|CI134565.1|CI134565
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTGACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|86595130|gb|CI260369.1|CI260369
EST:     CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG
EST: gi|88261592|gb|CI365168.1|CI365168
EST:     CTCAGTCCCCCTTGGTGG-ACAATTCTGAGGCAACCATTTGCAATCGGAG                         GTTCAGGCTGTAATTACCTCTATGGATTGCTTGACCACGAATGTAAGGAGG
genomic: CTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGG

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: 73 (upstream exon), 56 (downstream exon)
Score: 35

GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatat ... agttttgcagGTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatattatggcaaatgtctcttcattgggctcagagtaatctaatgggaaacatatttcccaccaacatttgtgtctatatataacatatctaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcccacc