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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttttcctgtaagctaatgttcatgtgaattttattgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA

Basic information

species Zea mays
transcript GRMZM2G010823_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 3
tagttttcctgtaagctaatgttcatgtgaattttattgtgaacctatcatgcttctgccaactgtgctatattg---tttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
   ||||    |    ||||  |||||| ||  ||| ||||| |  |   ||  |      |||||  ||| ||    ||| ||||||  |||   |||| |||| ||||||||||||||  ||||||| |||||||| ||||| || ||||||||||| ||||| ||||| |||||||| || ||||| || ||||||||||
--attttatcatgt-ttaattctcatgttaacattactgtgagctaagtttgtgttattatactgtaatatcttaccatttctgatctgcttttgcaatttagGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAGTTTGTACACCCTAATGATCATGTGAACAGATCACAGTCCTCAAATGATA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 3
tagttttcctgtaagctaatgttcatgtgaattttattgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaa---ttcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
|     | |||  || || || | ||   || |   ||||  |   |   | |    ||||| |||   | |  |    |  | | ||| | ||    ||||||| ||||||||  | ||| | ||||| ||||| || |||||||||| |||||| |||||||||||||||||||| ||||| || || ||||| |||||||
tgtggatactg--agttactgataataataactcctttgttcaatcacactacagtggccaattgtaa-aaacagaaagttttttttttcctgagcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGCGGTGGGAAGTTCGTGCACCCAAATGACCATGTCAATAGATCGCAGTCTTCTAATGATA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 3
tagttttcctgta-agctaatgttcat-gtgaattttattgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
|  | ||  |  | | |  || ||||| ||| |||  || |  ||   || ||  |  |    |||     ||    ||| |  | |||  ||    ||||||| ||||||||  | ||| | ||||| ||||| || ||||| |||||||||||||||||||||||||||||||| ||||| ||||| ||||| |||||||
ttatattaataaatatcccatcttcattgtgtattagatagataattcataatagtctttaagacttgagaatccattttcttttttctgatctt--ttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 3
tagttttcctgtaagctaatgttcatgtgaattttat--tgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaa---ttcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
   |  |  ||  |    || || || |  |||||||  | |  |    ||||  || |    |     ||  |   |  ||  ||| ||||| ||    ||||||| ||||||||  | ||| | ||||| ||| | || ||||| |||| |||||| |||||||||||||||||||| ||||| ||||| |||||||||||||
---tacttgtgataatacatatttatcttcattttatattatagatagttcataattgtattta--agacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 4
-tagttttcctgtaagct----aatgttcat-gtgaattttattgtg---aacctatcatg---------cttctgccaactgtgctatattgt-ttatgatctcttttccgaatt----cagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
 || |||   || |   |     |  |   | | | || | |||||    | |     |            |||||   |   |  |  ||| | || ||  ||  ||      |     ||||| ||||| ||||| ||| ||||||| ||||| | ||| || |||||||| | |||||||||||||||||||||||| || ||||||||||| || || |
gtaatttctttgcagtttttgagacatctgttgaggatctcattgtatatagctagctacaagagaaggctttctgtttatgttttttcattttcttttggccttgttatttgctcttcacagGTCATTGCTAATAGAGCAGCTGAGATTCTTGGTCGCAAACGTGGTGAGAAATGTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAACGACA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 2
tagttttcctgtaagctaatgttcatgtgaattttattgtgaacctatca--tgctt--ctgccaactgtgctatattgtttatgatctcttttccgaatt----cagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
         |   || |||   | ||   ||| | |      |  | | |  | |||  |  |||   || | |  |  || |  |  || |||     ||    ||||| ||||| ||||| ||| ||||||| ||||| ||||| || ||||| ||  ||||||||||||||||||||||||| || ||||||||||| ||||| |
--------ttaagagttaagactaattacaatgtcaaaaatgattttttagatacttaaccaccagacgtccgaggtaattaaacagatcattttgtgctttttacagGTCATTGCCAATAGAGCAGCTGAGATTCTTGGTCACAAACGTGGTGAAAAAATTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAATGACA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 4
------------tagttttcctgtaagctaatgttcatgtgaattttattgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
            |  ||| |||   | ||  | | | ||| | ||||  ||   |   ||  | |||||    | |  | | |||| ||||| | || |          ||||| ||||||||||| ||| ||||||| ||||| ||  |||| ||||| || | |||||| |||||||||||||| || || ||||||||||| |||||||
caggatttagtattctttgcctacgaactg-tatacttgtcatttttggtgatga---atattacttctttttatttggatttattttttatcaactgtgg--------cagGTTATTGCAAATAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 1
---tagttttcctgtaagctaatgttcatgtgaattttattgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
   ||||  ||   |    |  ||||  |    || || ||     | |  ||  |        ||     ||   |||||||   ||  ||      | ||||||||||||||||| ||| ||||||| ||||| ||||| || ||||| ||||| |||||||||||||| ||||| || || |||||||| |||||||| |
ttatagtcatctaattgttttctgttgttaattatcttgtttctttctttacacacacacatgcacacatataccatgtttattgactagttctt---tccagGTAATTGCAAATAGAGCAGCTGAGATTCTTGGCCACAAACGGGGTGAAAAGTTCGTGCACCCAAATGATCATGTCAACAGATCACAATCATCAAATGACA

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|211322399|gb|FL223776.1|FL223776
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|148999094|gb|EE030327.2|EE030327
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324568|gb|FL223785.1|FL223785
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324561|gb|FL223778.1|FL223778
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324560|gb|FL223777.1|FL223777
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|78111379|gb|DV529776.1|DV529776
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324571|gb|FL223788.1|FL223788
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|149089384|gb|EE178623.2|EE178623
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|149001505|gb|EE038811.2|EE038811
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211326730|gb|FL223797.1|FL223797
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324562|gb|FL223779.1|FL223779
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTGATTGCAAATAAGGCATCTGAGATCCTTGGGACACA-GCGCGGTGGAGA
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGG-ACACAAGCGCGGTG-AGA
EST: gi|211326731|gb|FL223798.1|FL223798
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324574|gb|FL223791.1|FL223791
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGNGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|148951891|gb|EC897665.2|EC897665
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324567|gb|FL223784.1|FL223784
EST:     NTATCTGGCNAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211326725|gb|FL223792.1|FL223792
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324570|gb|FL223787.1|FL223787
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324573|gb|FL223790.1|FL223790
EST:     TTATCTGGCAAACTGGNAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324572|gb|FL223789.1|FL223789
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324569|gb|FL223786.1|FL223786
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211326733|gb|FL223800.1|FL223800
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|91877250|gb|EB407207.1|EB407207
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211326737|gb|FL223804.1|FL223804
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211324565|gb|FL223782.1|FL223782
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211326729|gb|FL223796.1|FL223796
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAG                         GTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAG
EST: gi|211326736|gb|FL223803.1|FL223803
EST:     TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCNATGAG                         GTNATTGCAAATAGGGGCATCTGAAATCCTTGGACACAAGCCGCGGGTGAG
genomic: TTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGG-CATCTGAGATCCTTGGACACAAGC-GCGG-TGAG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 320

GGCAGCTGAGGAGGTCGCAGAGGGAAAGTTGGATGATCACTTCCCACTTGTTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

GGCAGCTGAGGAGGTCGCAGAGGGAAAGTTGGATGATCACTTCCCACTTGTTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 317

GGCAGCTGAGGAGGTCGCAGAGGGAAAGTTGGATGATCACTTCCCACTTGTTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

GGCAGCTGAGGAGGTCGCAGAGGGAAAGTTGGATGATCACTTCCCACTTGTTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgtcggtgtcc ... ccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
                                     tctcttttcc  CT-rich tract
                       tatattgtttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttttcctgtaagctaatgttcatgtgaattttattgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA

- - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - -gcttctg
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