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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttttcttccgcttctttgctagcctagctatatttaactgattattttgaaattgtcattcatgagtttttccctcaagcaattgttttcctc...

Basic information

species Oryza sativa
transcript LOC_Os01g69080.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G180399_T01 (Zea mays), 5'ss of exon 2
CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttttcttccgcttctttgctagcctagctatatttaactgattattttgaaattgt-cattcatgagtttttccctcaagcaattgttttcctc-----
|||||||||||| || || ||||| ||  | ||||||||||| ||||| || ||||| ||||||||||||||||||||||||||||||||||||||||||||||||  ||   ||   || |    |          ||||||||     |  |     |||| ||||||||         || |||   || |||||        
CAGGCATGGTGATCTTCTCAACAAGTACATGTACCTCACTGGGAGGGTAGATATGAGGCAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacatattctctctttttatccattttttcttacctatttaacatggcaagtctttcttgtacattcatg------cttctgaagtgtttattttcggttgctt

upper sequence: LOC_Os01g69080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G852502_T01 (Zea mays), 5'ss of exon 2
CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaaca-gttttct--tccgcttctttgct-agcctagctatatttaactgattattttgaaattgtcattcatgagtttttccctcaagcaattgttttcctc
|||||||||||| || || ||||| ||| | ||||||||||| |||||||| ||||| || |||||||||||||||||||||||||||||||||||||||||||||  || |||  |||  || ||| || || || |  | ||||       |  ||     || |||    |   ||||  | |   |  | | |  |    
CAGGCATGGTGATCTGCTCAACAAGTATATGTACCTCACTGGGAGGGTGGATATGAGGCAGATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacatattctctcatccatttttttactgagtcttgacacattttttcagct-cttcatgcttctcaagtgtttattttggcttgttgggagtttggtt---

upper sequence: LOC_Os01g69080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttttcttccgcttctttgctagcctagctat--atttaactgattattttgaaattgtcattcatg-agtttttccctcaagcaattgttttcctc
| | || || ||||| |||||||| ||  | ||| | || ||  | ||||||||||||||||| |||||||||||||||||  | ||||| ||||| ||||||| |       |   |  | |    |     | |      | ||    |      |  | ||| ||  | | |  ||      |   |    |||      
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgt-atctacgcaaattaaattgcgtacggaagttcgaa--

upper sequence: LOC_Os01g69080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagtttt-cttccgcttctttgctagcctagctatatttaactgattattttgaaattgtcattcatgagtttttccctcaagcaattgttttcctc
  | ||||| ||  | || ||||| |||||||||||||||||  | || |||||||  ||||| |||||||| || |||||  | || || ||||||||||||| ||      |||  |||  | |  | |  |   |  |     |    ||| |   |                                         
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttctttctcgggaactcaa--aagtcggtttttccattcttgcag----------------------------------------

upper sequence: LOC_Os01g69080.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttttcttccgcttctttgctagcctagctatatttaactgattattttgaaattgtcattcatgagtttttccctcaagcaattgttttcctc
  | ||||||||  | || ||||| |||||||||||||||||  | || |||||||  ||||| |||||||| || |||||  | || || ||||||||||||| ||          |||||||    |             |||| |  | || |   ||  ||||| |                              
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcggg------------aactcaaaagttcggtttttccattcttccag--------------------------

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|87005533|gb|CI287357.1|CI287357
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
EST: gi|58679461|gb|CK068148.1|CK068148
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
EST: gi|218493953|gb|FG957209.1|FG957209
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
EST: gi|218497416|gb|FG947812.1|FG947812
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
EST: gi|66915423|gb|CX102271.1|CX102271
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTAC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTAC
EST: gi|218478405|gb|FG958093.1|FG958093
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCT
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCT
EST: gi|58656047|gb|CK044727.1|CK044727
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
EST: gi|218478655|gb|FG958101.1|FG958101
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
EST: gi|218479656|gb|FG949097.1|FG949097
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
EST: gi|58598236|gb|CK008764.1|CK008764
EST:     ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: ACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC
EST: gi|58595027|gb|CF993335.1|CF993335
EST:     AATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATG                         GACCCTAGGACAGAGAACGATCCTTATCTTGGATTCATCTACACCTCCTTC
genomic: AATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTC

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: 73 (upstream exon), 57 (downstream exon)
Score: 51

CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttt ... tcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTCCAAGAGCGTGCGACCTTCATCTCACATGGGAACACTGCTCGCCATGCCA




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