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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCCTCGCCGACGCCGCCTACGTGAAGATCTCCGAGGGGGACTTCGGCTACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggccccctcccgacactcccttcccgttgcttcgattcgcaagctgctgctgcggtgatgctccgatcgttccggtttgtgatggcctttgcgt...

Basic information

species Oryza sativa
transcript LOC_Os05g44922.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44922.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 1
CAGCCTCGCCGACGCCGCCTACGTGAAGATCTCCGAGGGGGACTTCGGCTACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggccccctcccgacactcccttcccgttgct-tcgattcgcaagctgctgctgcggtgatgctccgatcgttccggtttgtgatggcctttgcgt
||||||||| |||||||||||||| |||||||||||||  ||||| || |||||||||||||||||||||||| ||  |||| ||||||||||   ||| ||||| |  | || |||  | | ||   | |    || ||  |    | ||   |  |  |||   |       ||   | ||  |   | ||  |  || 
CAGCCTCGCTGACGCCGCCTACGTCAAGATCTCCGAGGCCGACTTTGGATACGTCCTCGACGACGTGCCGCACTTCACCGACTACCTCCCCGACATCCCGgtgagcgcgctcccccctgcccgcctcccgcccccctgtctctgtagaggcgagtatttgggttgggggtgatgcgccacagtagggactagcggtgtcg-
















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|86831991|gb|CI305217.1|CI305217
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGAT
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGAT
EST: gi|117245202|gb|CT843402.1|CT843402
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCA                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|88360445|gb|CI608447.1|CI608447
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGAACAACTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGATCATCCAGCC
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCC
EST: gi|88411074|gb|CI606293.1|CI606293
EST:     ACGTCCTCGACGACGTGCCGCAACTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|58609232|gb|CK037265.1|CK037265
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCA                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|88360390|gb|CI612109.1|CI612109
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGGCCCC                         ACTTATCCCAATCCACCTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCAC-TACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|58668738|gb|CK057424.1|CK057424
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|87015409|gb|CI303015.1|CI303015
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTA
EST: gi|88344168|gb|CI626712.1|CI626712
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCC-GATGCCCCC                         ACTTATCCCAATC
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATC
EST: gi|88362351|gb|CI608742.1|CI608742
EST:     ACGTCCTCGACGACGTGCCGTACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCC-AATCCACTA-AAGATCATCC
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCC
EST: gi|88343176|gb|CI627136.1|CI627136
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATC
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATC
EST: gi|88399416|gb|CI606037.1|CI606037
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCAC-TCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGATCATCAAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|88398058|gb|CI585561.1|CI585561
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAGC
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAGC
EST: gi|58606730|gb|CK034763.1|CK034763
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCA                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|88395276|gb|CI611193.1|CI611193
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|58671614|gb|CK060300.1|CK060300
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|58671004|gb|CK059690.1|CK059690
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA
EST: gi|88395278|gb|CI611195.1|CI611195
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCC-AATCCACTACAAGATCATCCAGCCTATTCAACTGTC
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTC
EST: gi|86850574|gb|CI309386.1|CI309386
EST:     ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCC                         ACTTATCCCAATCCACTACAAGAT
genomic: ACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGAT

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: 62 (upstream exon), 47 (downstream exon)
Score: 13

CAGCCTCGCCGACGCCGCCTACGTGAAGATCTCCGAGGGGGACTTCGGCTACGTCCTCGACGACGTGCCGCACCTCGTCGACCACCTCCCCGATGCCCCCgtgagtggcc ... atatgtgcagACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA




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