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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcattgatacagaatgattctgacctctcatcccatgattcattgatgcgaaatgatcaacttgatttccggtttgatatctaatagcatgcaaaagtagggggaaagtggaatactagaatcattgtagtttattctacaattaacattgcagagtgttgtaaatcttcctttaatttttcttattttgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCCTACTTACTGGGATTTGTTG

Basic information

species Oryza sativa
transcript LOC_Os01g10340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G871861_T02 (Zea mays), 3'ss of exon 3
gtgcattgatacagaatgattctgacctctcatcccatgattcattgatgcgaaatgatcaacttgatttccggtttgatatctaatagcatgcaaaagtagggggaaagtggaatactagaatcattgtagtttattctacaattaacattgcagagtgttgtaaatcttcctttaatttttcttattttgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCCTACTTACTGGGATTTGTTG
||  ||||||   | ||||| ||    ||| |||   ||  |||||||| | |||| |   | |    ||  ||||          |||  || |     ||        |  ||||||  |   ||| |      || |  |||| ||| || |              |||||||  || ||      |     ||||||| |||||||||||||||||||||||||| ||||  |||||| |  |  ||||||| ||||||||| |||
gtttattgatgtgggatgatcctattttcttatctattg--tcattgatcccaaataaaataataatcttgtggtta------ctgtagactgtag----agcatcttgtttcaatactgcagctattat------ttgtggaattgacaatgtaa-------------ttccttt--ttctttccccctcacgttgtagGGTTTATTGCTGGCAGTTACTTTGGTTATTGATTGGTGGCTGGCCTTTGCCTACTTTCTGGGATTTCTTG
















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|88572533|gb|CI664104.1|CI664104
EST:     AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAG                         GGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
genomic: AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAGgtgcattgat ... tgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
EST: gi|88329003|gb|CI658653.1|CI658653
EST:     AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAG                         GGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
genomic: AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAGgtgcattgat ... tgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
EST: gi|88342680|gb|CI657174.1|CI657174
EST:     AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAG                         GGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
genomic: AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAGgtgcattgat ... tgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
EST: gi|88401880|gb|CI591207.1|CI591207
EST:     AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAG                         GGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
genomic: AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAGgtgcattgat ... tgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
EST: gi|88308193|gb|CI648020.1|CI648020
EST:     AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAG                         GGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
genomic: AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAGgtgcattgat ... tgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
EST: gi|88693166|gb|CI736741.1|CI736741
EST:     AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAG                         GGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC
genomic: AAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAGgtgcattgat ... tgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCC

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: 64 (upstream exon), 54 (downstream exon)
Score: 17

ATCGTGAAAGAGGAAAACTGGGAAACATGCATTGCTGATTCACTGCTCTATGCTAAGgtgcattgat ... tgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCCTACTTACTGGGATTTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacattgcagagtgttgtaaatcttcctttaatttttcttattttgatctgtagGGATTATTGCTGGCAGTTACTTTGGTTATCGATTATTGGCTGACTGTCTCCTACTTACTGGGATTTGTTG
                      tcttcctttaattttt  CT-rich tract
                  taaatcttcctttaat  TA-rich tract