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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatggcgctcgatcggtcaagctttcattacgatgtagcagcgcgccgcgccagccattagttggcttggactactcatggcgtcttgattaattagtcgatctcactcgcgacgtcgtcgtctcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCTCGACCTGTCGGACTGGCTCGACACGAGGAACGCCGCCTACGACATCTAC

Basic information

species Oryza sativa
transcript LOC_Os03g13520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G152390_T06 (Zea mays), 3'ss of exon 2
----gtacatatggcgctcgatcggt-caagctttcattacgatgtagcagcgcgccgc-gccagccattagttggcttggactactcatggcgtcttgattaattagtcgatctcactcgcgacgtcgtcgtctcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCTCGACCTGTCGGACTGGCTCGACACGAGGAACGCCGCCTACGACATCTAC
    ||| ||||    ||  |    | | |      |  ||    | | ||   || || ||||||||  ||| |     | |      |    |  || |      | || |   |     |   | ||  |   | |||||||||||||||||||||||||||||| |||||||| |||||||||||||  || ||||||||||||||||| |||                           
gtatgtatatatactcctatacgaatacgacacgatagaacacgatcggag-aagctgcagccagccaa-agtcgagagtgccgctagctaatctgctgctggcgccgccg-ttatatatatgggtttgttttggtggctgcagGCTGTTCGCGAGCACGTGGAACGTGGGCGGCGTGGCGCCACCGGACGGGCTGGACCTGTCGGACTGGCTGGACGGCG-----------------------

upper sequence: LOC_Os03g13520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G178279_T01 (Zea mays), 3'ss of exon 2
------------------------gtacatatggcgctcgatcggtcaagctttcattacgatgtagcagcgcgccgcgc-cagccattagttggcttggactactcatg-------gcgtcttgatt-------aattagtcgatctcac-tcgcgacgtcgtcgtctcgtctg--------cagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCTCGACCTGTCGGACTGGCTCGACACGAGGAACGCCGCCTACGACATCTAC
                        || ||   |         |   || |  ||| | | |  | || || | |||| |     | | | | ||       || ||  ||         |||   ||        | | ||   | ||  | || ||   |||||  || |  |         |||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||||||||| |||    |   || || | |||||  |   
gtacgtgcttctcctattggccatgtgcactcgagcagtagccaaccatgtattcctcagggag-aggagagagccgtgagtgactactggctgctgcctgctgctgctgtggaagaaagtcaaaatcgccgctaagtaagctaaactggcgtctcgctatcgtctgctggcatatggcatatcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTGGCGCCACCGGACGAGCTGGACCTGTCGGACTGGCTGGACGGCGGCGGCGGCGACGACGACGACGGG

upper sequence: LOC_Os03g13520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G152390_T04 (Zea mays), 3'ss of exon 2
----gtacatatggcgctcgatcggt-caagctttcattacgatgtagcagcgcgccgc-gccagccattagttggcttggactactcatggcgtcttgattaattagtcgatctcactcgcgacgtcgtcgtctcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCTCGACCTGTCGGACTGGCTCGACACGAGGAACGCCGCCTACGACATCTAC
    ||| ||||    ||  |    | | |      |  ||    | | ||   || || ||||||||  ||| |     | |      |    |  || |      | || |   |     |   | ||  |   | |||||||||||||||||||||||||||||| |||||||| |||||||||||||  || ||||||||||||||||| |||    |  ||| || |     |  | ||
gtatgtatatatactcctatacgaatacgacacgatagaacacgatcggag-aagctgcagccagccaa-agtcgagagtgccgctagctaatctgctgctggcgccgccg-ttatatatatgggtttgttttggtggctgcagGCTGTTCGCGAGCACGTGGAACGTGGGCGGCGTGGCGCCACCGGACGGGCTGGACCTGTCGGACTGGCTGGACGGCGGCGACGACGACGGGCCCTACGAC

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|29640434|gb|CB645443.1|CB645443
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|88393484|gb|CI619776.1|CI619776
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|29670691|gb|CB666966.1|CB666966
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|29634762|gb|CB639771.1|CB639771
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|29661801|gb|CB658076.1|CB658076
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|29671559|gb|CB667834.1|CB667834
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|117222224|gb|CT845752.1|CT845752
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|29634757|gb|CB639766.1|CB639766
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGCTCGCGAGCACGTGGAA
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAA
EST: gi|29671784|gb|CB668059.1|CB668059
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|29668856|gb|CB665131.1|CB665131
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
EST: gi|58688536|gb|CK077223.1|CK077223
EST:     CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAG                         GCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT
genomic: CCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCT

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: 44 (upstream exon), 39 (downstream exon)
Score: 3

ACGACGATGGTTGCAGCCCCGACGCCGACGCCTGCCGCAGCGTGAAGCGGCCGCGGCCGCGGCCGCAGCAGCGAGCGAGCAACAAGACGCTCAAGTACAGgtacatatgg ... tcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCTCGACCTGTCGGACTGGCTCGACACGAGGAACGCCGCCTACGACATCTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcgtcttgattaattagtcgatctcactcgcgacgtcgtcgtctcgtctgcagGCTGTTCGCGAGCACGTGGAACGTCGGCGGCGTCGCGCCACCGGACGACCTCGACCTGTCGGACTGGCTCGACACGAGGAACGCCGCCTACGACATCTAC
                      atctcac  putative branch site (score: 3)
                                           tctcgtct  putative PPT
       ttgattaatta  TA-rich tract