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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGATAATAGCTGTGCCGGCCTTCAGTACCCTAAGATGAAACTTTTGTCTCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttccttgaacaatatagtacttctagagaaaagtgttgtaccaacacaacttgtgttatcactgttaagtgttgattttactaatcctgtttcttgtgctttacag

Basic information

species Oryza sativa
transcript LOC_Os02g47850.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47850.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G147450_T03 (Zea mays), 5'ss of exon 11
AACGATAATAGCTGTGCCGGCCTTCAGTACCCTAAGATGAAACTTTTGTCTCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttccttgaacaatatagtacttctagagaaaagtgttgtaccaacacaacttgtgttatcactgttaagt-gttgattttactaatcctgtttcttgtgctttacag
||||| ||||| ||||| |||||||||||| | |||||||| ||| ||||||| ||||||||||| ||||| || || || ||||||||||| |||   ||||||||| |||   | | |   | ||  |     |   || ||||  |||  |   ||   | | | ||| |  | | |||| |  | | ||  || | |||||||||||||
AACGACAATAGTTGTGCTGGCCTTCAGTACGCCAAGATGAAGCTTGTGTCTCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttcttttgctagaatcttctgttgatccaccatggtgtag-aacgta--ctgctatcttaatgtgatttagctgatgtctcgattc--gtcttttgtgctttacag

upper sequence: LOC_Os02g47850.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G029573_T01 (Zea mays), 5'ss of exon 10
AACGATAATAGCTGTGCCGGCCTTCAGTACCCTAAGATGAAACTTTTGTCTCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttccttgaacaatatagtacttctagagaaaagtgttgtaccaacaca-acttgtgttatcactgttaagtgttgattttactaatcctgtttcttgtgctttacag
||||||||||| || || ||||| |||||| | |||||||| ||| ||||||| ||||||||||| ||||| || || || |||||||| || |||   ||||| |||| |  |  |  ||    |||||| |||       || |  |  ||   ||||   | | | ||| |  |      | ||   || |  | | ||||| |||||||
AACGATAATAGTTGCGCTGGCCTCCAGTACTCCAAGATGAAGCTTATGTCTCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttcttgtactagaat----cttctatagatccaccatggagtacaacgtgcttgctatcttaatgtgatttagctgatgtatcgattc-atgttttgtgttttacag
















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|88365911|gb|CI545770.1|CI545770
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88385064|gb|CI561720.1|CI561720
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|89176288|gb|CI043309.1|CI043309
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|58661834|gb|CK050514.1|CK050514
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88250235|gb|CI348465.1|CI348465
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTTAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|25803551|gb|CA759512.1|CA759512
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|86880519|gb|CI321005.1|CI321005
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGGAG-TGATGAAGAACAACAGATTGTGAGGCGCA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATA-GAGATGATGAAGAACAACAGATTGTGAGGCGCA
EST: gi|88468047|gb|CI517506.1|CI517506
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88274055|gb|CI394461.1|CI394461
EST:     CCATCCAGAGTCCTCACCCGGGCCGCATGATTCTTACTTGG                         CTTTT-GTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: CCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88268554|gb|CI378489.1|CI378489
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTGTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGGCA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCG-CA
EST: gi|88266357|gb|CI377259.1|CI377259
EST:     TCTTCACTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88975138|gb|CI023389.1|CI023389
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88232225|gb|CI230683.1|CI230683
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|88322108|gb|CI537691.1|CI537691
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGNCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
EST: gi|86482764|gb|CI125397.1|CI125397
EST:     TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGG                         CTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA
genomic: TCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAA

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: 69 (upstream exon), 73 (downstream exon)
Score: 101

AACGATAATAGCTGTGCCGGCCTTCAGTACCCTAAGATGAAACTTTTGTCTCTTCAGTACCATCCAGAGTCCTCACCCGGGCCGCATGATTCTGACTTGGgtacatttcc ... tgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAAATATAAGATACAAGGGTTTGGTTCTTGAACCGGGAGGTGAGAGGTTCTA




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