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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGATAGTTTGTCTGCAAAGGACGACAGTGGCAAGGACTGGTCTTTCATTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatgctttaaattttcacagataacacttccattcttctatcgactggtgatttctccatatataatgtgactgcaaacactgcaattcacacaatacactaagtattcttaatttgattcgtttgtatttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g55420.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G836910_T01 (Zea mays), 5'ss of exon 10
TTATGATAGTTTGTCTGCAAAGGACGACAGTGGCAAGGACTGGTCTTTCATTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatgctttaaatttt--cacagataacacttccattcttctatcgact--ggtgatttctc-catatataatgtgactgcaaacactgcaattcacacaatacactaagtattcttaatttgattcgtttgtatttgcag
 || || ||||||||||| |||||| | || |||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||| | ||||| ||   |||||    || |  ||  |   | || ||      |  ||| | |    | |    || || |     |||     || |||   ||  |   | || | |      || | ||||||   |  || ||   |||||
CTACGACAGTTTGTCTGCCAAGGACAAGAGCGGCAAGGACTGGTCTTTCATTCTGAGGCAGATTGGCATGTTCTCCTACACCGGCTTGAACAAAGCGCAGgtaacgc-tgcttccgcttgtgccattgtgcagacatcacgcgctaaatcaagttcaatcaccggtcacacactctttgttgaaacatacatatcatctacaaaaaaataacgtaaatgcataatttcgctttttcgt--ctgcag

upper sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA14G13480.1 (Glycine max), 5'ss of exon 10
TTATGATAGTTTGTCTGCAAAGGACGACAGTGGCAAGGACTGGTCTTTCATTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacata-------tgctttaaattttcacagataa-cacttccattcttctatcgactg-gtgatttctccatatataatgtgactgcaaacactgcaattcacacaatacactaagtattcttaatttgattcgt---ttgtatttgcag-----------
 ||||||||| |  || |||| ||| | ||||| ||||| ||||| ||||| || | |||||||||||||||||| | ||||||||||||||  |  ||||| |   |       |  |  || || |  ||  | | ||  |     ||| |||  |||  ||    ||    |  ||    | | || |||||  |    |   ||| ||   ||| ||||     | |  ||| |   |  ||| |   |           
ATATGATAGTATTACTTCAAAAGACAAAAGTGGAAAGGATTGGTCATTCATACTTAAGCAGATAGGCATGTTCTCATTCACGGGCTTGAACACGAACCAGgtaattgactactgttattacaacttcttgcatgtgatcaacttgtggcttttatacactatgttgagtcctatttcattgactaaatgaaaacatcgtcgattttacagtattgtaa-tattgactgtcttgttcttaaatgatatcttgtgtctctcatcag

upper sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA17G33050.4 (Glycine max), 5'ss of exon 10
TTATGATAGTTTGTCTGCAAAGGACGACAGTGGCAAGGACTGGTCTTTCATTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatgctttaaattttcacagataacacttccattcttctatcgactggtgatttctccatatataatgt-gactgcaaacactgcaattcacacaatacactaagtattcttaatttgattcgtttgtatttgcag
 ||||||||| |  || |||| ||| | ||||| ||||| ||||| ||||| || | |||||||||||||||||| | ||| ||||||||||| |  ||||| |    || || |  || | |        |||||     |  |||| ||| |||  || |  ||| |  |||| || | | |   |    | |    ||| | | | | |||  |    || | |  | | |  |     
ATATGATAGTATTACTTCAAAAGACAAAAGTGGAAAGGATTGGTCATTCATACTTAAGCAGATAGGCATGTTCTCATTCACTGGCTTGAACAAGAACCAGgtaat---tgattcatgttattatg------acttcttgcatgttatcaacttgtggctttt--atacactatgttgagtcctatttcattgactatatcaacatattgactatgttgttcttaaatgatatctcatcag--

upper sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 5'ss of exon 11
TTATGATAGTTTGTCTGCAAAGGACGACAGTGGCAAGGACTGGTCTTTCATTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgt--gacatatgctttaaattttcacagataacacttccattcttctatcgactggtgatttctc-catatataatgtgactgcaaacact-gcaattcacacaatacactaagtattcttaatttgattcgtttgtatttgcag
 ||||||||  |   | |||| ||| | || || ||||||||||| |||||||||| ||| || ||||||||||| | ||| ||| | |||||| |||||||  | ||     |||||   | |||||||    | |     ||| | | |||| ||| |||      | |    | |   |      ||  |||                                                  
GTATGATAGCCTCGTTTCAAAAGACAAGAGCGGGAAGGACTGGTCCTTCATTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAGgtatgccaacaattttaatactacacagat--tccctttggccttgtttagacttgtggtttgaagtttgtgctgttttcttttggtaacgagcag-------------------------------------------------

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|86873530|gb|CI329908.1|CI329908
EST:     TTCTGAGCCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88985190|gb|CI006844.1|CI006844
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88544893|gb|CI472420.1|CI472420
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACGAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|33807024|gb|CF329393.1|CF329393
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88527234|gb|CI455371.1|CI455371
EST:     GGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGGATGGGAG
genomic: GGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAA-GGATGGGAG
EST: gi|4968812|gb|AU065716.1|AU065716
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88471399|gb|CI408670.1|CI408670
EST:     GATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATGCATGACAAAGGATGGGAGA
genomic: GATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88382581|gb|CI535789.1|CI535789
EST:     GGCTTGNACCAAACTCAG                         AGTGATAATATGGCCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: GGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|29666647|gb|CB662922.1|CB662922
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|29289873|gb|CB483487.1|CB483487
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCCTGAACAAAACTCAG                         AGTGATAATACGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|86873298|gb|CI341523.1|CI341523
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88380490|gb|CI518860.1|CI518860
EST:     CACGGGCTTGGACGAAACTCAG                         GGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: CACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|11442628|gb|BF430531.1|BF430531
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88374663|gb|CI518530.1|CI518530
EST:     TTGTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACGAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88543173|gb|CI473160.1|CI473160
EST:     TCCTACACGGGCTTNAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|86594945|gb|CI258199.1|CI258199
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|86251834|gb|CI019026.1|CI019026
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACCAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|86599210|gb|CI355827.1|CI355827
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88511573|gb|CI439079.1|CI439079
EST:     TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAG                         AGTGATAATATGACCGACAAATGGCACATATGCATGACAAAGGATGGGAGA
genomic: TTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA
EST: gi|88544038|gb|CI474099.1|CI474099
EST:     AGATAGGCATGTTCTCCTACACGGGGTTGAACAAAAGTCAG                         AGTGATAATATGACCGACCAAGGGCACATATACATGACAAAGGATGGGAGA
genomic: AGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGA

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: 71 (upstream exon), 72 (downstream exon)
Score: 130

TTATGATAGTTTGTCTGCAAAGGACGACAGTGGCAAGGACTGGTCTTTCATTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatg ... gtatttgcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGAATTTCGTTGGCTGGATTGTCCCTGGCTAAATGCGAGTACCTAGCTGACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGATAGTTTGTCTGCAAAGGACGACAGTGGCAAGGACTGGTCTTTCATTCTGAGGCAGATAGGCATGTTCTCCTACACGGGCTTGAACAAAACTCAGgtgacatatgctttaaattttcacagataacacttccattcttctatcgactggtgatttctccatatataatgtgactgcaaacactgcaattcacacaatacactaagtattcttaatttgattcgtttgtatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT