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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGGGAGAGGAAAATACAGCGAGGTCTTTGAGGGTATTAATGTCAACAACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatgattcatgaatcctgttgtccatcctttttttccttttcccctgaacatgctcttttactggtaacatggtactgtttccatcttacacctagctttgtgtcaatggcattagtgtttattattttaaccatagttttcttttgtatgcag

Basic information

species Oryza sativa
transcript LOC_Os07g02350.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 2
AGTTGGGAGAGGAAAATACAGCGAGGTCTTTGAGGGTATTAATGTCAACAACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatgattcatgaatcctgttgtccatcctttttttccttttcccctgaacatgctcttttactggtaacatggtactgtttccatcttacacctagctttgtgtcaatggcattagtgtttattattttaaccatagttttcttttgtatgcag
 || ||||||||||||||||| || || ||||| ||||||||||| ||||| ||||| |||||||| ||||| || ||||||||||||||||||||||||||||   ||||   ||    ||||   |   |   || ||      |||||||||| | || ||||||   | ||| | |||||||| |||   |||| |      || | |||  ||| | |     | |||||||||   |  |  |  ||  || ||
GGTCGGGAGAGGAAAATACAGTGAAGTATTTGAAGGTATTAATGTTAACAATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatgaactatatcacctgccctttgtaacttgtta-----tcccctgaacctactattttaccaatgacaggctactgttttcattccacacat------gtttaaatttcataatttcaattgattttaacctatgcctcgtgctg-gtgtag

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 2
AGTTGGGAGAGGAAAATACAGCGAGGTCTTTGAGGGTATTAATGTCAACAACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatgattcatgaatcctgttgtccatccttttt--ttccttttcccctgaacatgctcttttactggtaacatggtactgtttccatcttacacctagctttgtgtca--atggcattagtgtttattattttaaccatagttt-tcttttgtatgcag------
|||||||||||| |||||||| || |||||||||||||||||||| ||||| ||||| |||||||| || || || ||||||||||||||||||||||||||||         |||||||||| ||||      |||     |  || |||||||||| | || |||||  ||| ||| | |||||||| | | | ||||||   |   | |||  ||  || |     || | || | |    ||   | |  ||  | ||| |      
AGTTGGGAGAGGGAAATACAGTGAAGTCTTTGAGGGTATTAATGTTAACAATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagac-------catgaatcctattgtatgcagtttgcaacttgttatcccctgaacctactattttagcggtgacaggctactgttttcttttcacacctgtttaaatttcataatttcagtgacaattttcatctcagttttaacatatgcttcttgtgctggtgcag
















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|29661177|gb|CB657452.1|CB657452
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|58591038|gb|CF989346.1|CF989346
EST:     ACAATGAAACATGCGTTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCACAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|117220732|gb|CT845509.1|CT845509
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|58691077|gb|CK079764.1|CK079764
EST:     AGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: AGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|58658866|gb|CK047546.1|CK047546
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|88362961|gb|CI614317.1|CI614317
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAACAATA
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATA
EST: gi|58659986|gb|CK048666.1|CK048666
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|2317607|gb|C22661.1|C22661
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|58593999|gb|CF992307.1|CF992307
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCCAAAGAGAGATTAAAATACTTCAGAATCTTTGTGGAGGTCCCAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|29663346|gb|CB659621.1|CB659621
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|2317323|gb|C22377.1|C22377
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGNAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|29657465|gb|CB653740.1|CB653740
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCCAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|428809|gb|D24965.1|D24965
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|58600654|gb|CK011182.1|CK011182
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATCACAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|29662230|gb|CB658505.1|CB658505
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|58653242|gb|CK041922.1|CK041922
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|11442779|gb|BF430681.1|BF430681
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|27577759|gb|CB000454.1|CB000454
EST:     AATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGACGTAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: AATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|58681564|gb|CK070251.1|CK070251
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|5607464|gb|AU076249.1|AU076249
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC
EST: gi|218485894|gb|FG960234.1|FG960234
EST:     ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAGATATAAATACTTCAGAATCTTGGTGGAGGTCCAAATATC
genomic: ACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATC

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), 64 (downstream exon)
Score: 62

AGTTGGGAGAGGAAAATACAGCGAGGTCTTTGAGGGTATTAATGTCAACAACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatg ... ttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATCGTGAAACTGCTTGATATTGTTAGAGATCAGCACTCAAAAACACCAAGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGGGAGAGGAAAATACAGCGAGGTCTTTGAGGGTATTAATGTCAACAACAATGAAAAATGCATTATCAAAATTCTCAAGCCTGTGAAGAAAAAGAAGgtagttcatgattcatgaatcctgttgtccatcctttttttccttttcccctgaacatgctcttttactggtaacatggtactgtttccatcttacacctagctttgtgtcaatggcattagtgtttattattttaaccatagttttcttttgtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG