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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCGAAGCGTCAATTTTAAATTCTCTGAAGACTTTGTCCGTTGACCGTACCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgttcatgcaaatacattagaacaaaaaaacctgcaacttcattttgtgaaagtaatatgatttattgaactaaaaatagggattcagagtaa...

Basic information

species Oryza sativa
transcript LOC_Os06g03770.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03770.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G032936_T01 (Zea mays), 5'ss of exon 14
CACCGAAGCGTCAATTTTAAATTCTCTGAAGACTTTGTCCGTTGACCGTACCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgttcatgcaaatacattagaa-caaaaaaacctgc--aacttcatt---ttgtgaaagtaatatgattta--ttgaactaaaaatagggattcagagtaa--------------
 || ||||| |||||||| |||||||||||  | || ||    || || || || ||||||||||| |||||||| |||||||||||||| |||||| ||||| ||    |  ||||| | |   |||| | | |  || |    ||  ||| |   | ||||| ||    || ||||   |   || ||  |     || |   |                
TACTGAAGCATCAATTTTGAATTCTCTGAAATCCTTATCTTCCGATCGAACATCAATCTTTATTGCTCATCGACTCACAACTGCAATGCAGTGTGATCAGgtacgc----ttctgcaacttctccagaaaccatagtacgttttgaatgtcagtaaatggtgaatgttggttggtttaatcttgtctcaagtttttttttgatgattcctctttattttcag

upper sequence: LOC_Os06g03770.1 (Oryza sativa), 5'ss of exon 19
lower sequence: PP1S249_41V6.1 (Physcomitrella patens), 5'ss of exon 21
CACCGAAGCGTCAATTTTAAATTCTCTGAAGACTTTGTCCGTTGACCGTACCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgttcatgc---aaatacattagaacaaaaaaacctgcaacttcattttgtga----aagtaatatgat--ttattgaactaaaaatag-ggattcagagtaa--------------------------------------------------------
 || || |     || || | | | |||    | ||  ||  |||||| || ||||||||||| || |||||| | ||||| |||||||| |||||||||||    || | |||||    ||   | ||||| |  | ||  |  |  |  | | ||  |      | | | ||||  | ||||   |  |      | || |  ||                                                           
AACTGAGGGAGAGATCTTGACTGCGCTGCGATCGTTAGCCAATGACCGAACTTCTATCTTTATCGCCCATCGATTAACAACAGCAATGCAGTGTGATGAGgtgaaaatttgcatgccaggaactaagtagaagagtagaaagtttagttcaagtgtgctattttgcggagtctgatcctcattgggttttagtcgttgaatgctaagatgctggtgtacttggtttgttgtgattcacttgcctcgatcgattttcgttgctgcag
















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|86429794|gb|CI082217.1|CI082217
EST:     CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|88234720|gb|CI234569.1|CI234569
EST:     CATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|86478407|gb|CI121040.1|CI121040
EST:     CCTCTATCTTTATTGCACGTCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACTACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|218503707|gb|FG953305.1|FG953305
EST:     CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|86828024|gb|CI274925.1|CI274925
EST:     CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|38480897|gb|CF964986.1|CF964986
EST:     CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|29670311|gb|CB666586.1|CB666586
EST:     CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|218481604|gb|FG953916.1|FG953916
EST:     CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTATTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|86425236|gb|CI070333.1|CI070333
EST:     CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|88544490|gb|CI472593.1|CI472593
EST:     TTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: TTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
EST: gi|29646656|gb|CB651663.1|CB651663
EST:     CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAG                         ATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT
genomic: CCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTT

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), 58 (downstream exon)
Score: 7

CACCGAAGCGTCAATTTTAAATTCTCTGAAGACTTTGTCCGTTGACCGTACCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgt ... gtattttcagATTATTGTTTTGGAGAATGGGGAGGTAGTGGAACAAGGACCACATGATTTTCTGCTGTCAAAGGGTGGCCGATATGCTGAATTGTGGTCACAGCAGAATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCGAAGCGTCAATTTTAAATTCTCTGAAGACTTTGTCCGTTGACCGTACCTCTATCTTTATTGCACATCGACTGACAACTGCAATGCAATGTGATGAGgtatgcatgttcatgcaaatacattagaacaaaaaaacctgcaacttcattttgtgaaagtaatatgatttattgaactaaaaatagggattcagagtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata