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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtattaatactctgcagatttattcccagtaaagcaggtgatgtttatttgaactcaggtatgattattacatttgctacatactgcag

Basic information

species Oryza sativa
transcript LOC_Os07g39630.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g39630.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G066051_T01 (Zea mays), 5'ss of exon 9
GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtattaatactctgcagatttattcccagtaaagcaggtgatgtttatttgaactcaggtatgattattacatttgctacatactgcag
||||| || |||||||||||||||||||||||||| |||||||||||  || |||| |  ||  | || | ||          ||    | |||   || ||||||  | | ||| | |||||    |   |  ||||
GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgt-ttaacaaccttaacatctttttt------gtcaacaaaagttcgcttaaactcattttttattgt-acatt----atgcatcgcag
















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|88219747|gb|CI219307.1|CI219307
EST:     GAGAGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAGCTGAGGTTGTAAACATACTAGTC
genomic: GAGAGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|38473913|gb|CF958045.1|CF958045
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|58598860|gb|CK009388.1|CK009388
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGGGAGGATAAAAACAAGCCAACTGAGGTTGTAAACATACTAG
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGC-GGCA-AATAAAAACAAGCCAACTGAGGTTGTAAACATACTAG
EST: gi|86528760|gb|CI168966.1|CI168966
EST:     CATGTGTTCAAG                         TTATTTGCGGCAAATAAAGACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: CATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|29675062|gb|CB671337.1|CB671337
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|218481593|gb|FG960934.1|FG960934
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|29673566|gb|CB669841.1|CB669841
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|86500993|gb|CI143626.1|CI143626
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|88226063|gb|CI225979.1|CI225979
EST:     GATTCAAGCCAAAATATTCAAATGTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATATATACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAAT-TGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|38481075|gb|CF965164.1|CF965164
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|88214576|gb|CI214425.1|CI214425
EST:     ATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: ATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|29673647|gb|CB669922.1|CB669922
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|89170800|gb|CI040077.1|CI040077
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGT
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGT-GTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGT
EST: gi|88490037|gb|CI427309.1|CI427309
EST:     TGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: TGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|29679531|gb|CB675806.1|CB675806
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|87008328|gb|CI301086.1|CI301086
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|29664684|gb|CB660959.1|CB660959
EST:     GATTCAAGC-AAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|58663168|gb|CK051854.1|CK051854
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|25799534|gb|CA755495.1|CA755495
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|29656023|gb|CB652298.1|CB652298
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|66915714|gb|CX102562.1|CX102562
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|58688748|gb|CK077435.1|CK077435
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|29660229|gb|CB656504.1|CB656504
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
EST: gi|86426306|gb|CI071403.1|CI071403
EST:     GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG                         TTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC
genomic: GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTC

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: 48 (upstream exon), 69 (downstream exon)
Score: 79

GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtatta ... catactgcagTTATTTGCGGCAAATAAAAACAAGCCAACTGAGGTTGTAAACATACTAGTCACAAACCGAAGCAAGCTTCTCCGATTTTTTGCCGGATTCAAGATTGACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtattaatactctgcagatttattcccagtaaagcaggtgatgtttatttgaactcaggtatgattattacatttgctacatactgcag

- -  AAGCAA
- - - - - - - - - - - TTGAAG
- - - - - - - - - - -  TGAAGC