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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttcttttgggggatttcttggcgttcgttctgtttgagaatttttggggggcgggtttcctgaatttggttggacctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATCCGCTGGTACATTGAGTTGGAGGACGGCTACTTGGTCGAGCAGGAGAAGC

Basic information

species Oryza sativa
transcript LOC_Os04g53760.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53760.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 1
gtgggttcttttggggg-atttcttggcgtt-----cgttctgtttgagaatttttggggggcgggtttcctgaatttggttggacctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATCCGCTGGTACATTGAGTTGGAGGACGGCTACTTGGTCGAGCAGGAGAAGC
||||| | |    |    ||||  ||  |        ||  | ||   |    ||||  ||| | ||| |||  | |||||      | |||||||||||   || |||||||| || |||||||||||||| || || |||||||| |||||||| ||| ||||||| ||||| ||||  |||||||||||||
gtggggtttcggagctttatttactgaagacgaagatgtgttattgatgcggatttgtcgggagcgttcccttgaattggtcctgtttctgcagGGGAGAGTCGATCAGATGAGCGACTACATCAAGAAGCTCAGGGCGTGCATCCGGTGGTACATGGAGCTGGAGGATGGCTATTTGGCTGAGCAGGAGAAGC
















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|88386555|gb|CI575333.1|CI575333
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88371328|gb|CI600176.1|CI600176
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88449325|gb|CI582197.1|CI582197
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88389664|gb|CI603163.1|CI603163
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGATTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|29623653|gb|CB628664.1|CB628664
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|29635281|gb|CB640290.1|CB640290
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAC                         GGGAGAACTGAGCATATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88300304|gb|CI584723.1|CI584723
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88422750|gb|CI573912.1|CI573912
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88386498|gb|CI575276.1|CI575276
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88403245|gb|CI570986.1|CI570986
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88385811|gb|CI568479.1|CI568479
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACA-G                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88430893|gb|CI571883.1|CI571883
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88427363|gb|CI569401.1|CI569401
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACCAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88362880|gb|CI614236.1|CI614236
EST:     AGCGGCTGCTCGCCGACAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAA-TGAG
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAG
EST: gi|88399908|gb|CI585827.1|CI585827
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
EST: gi|88454426|gb|CI569998.1|CI569998
EST:     AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAG                         GGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC
genomic: AGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATC

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: 72 (upstream exon), 46 (downstream exon)
Score: 13

GGCTGGGCCGGCGGCGCCTGTGATCGAGTTCACCGGGAGGGAGGATGTGGAGCGGCTGCTCGCCGAGAAGATGAAGGGGAAGAGCAAGACCGACTACAAGgtgggttctt ... acctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATCCGCTGGTACATTGAGTTGGAGGACGGCTACTTGGTCGAGCAGGAGAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttgagaatttttggggggcgggtttcctgaatttggttggacctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATCCGCTGGTACATTGAGTTGGAGGACGGCTACTTGGTCGAGCAGGAGAAGC
        agaattttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttcttttgggggatttcttggcgttcgttctgtttgagaatttttggggggcgggtttcctgaatttggttggacctgtgcagGGGAGAACTGAGCAGATGAGTGAGTACATCAAGAAGCTGAGAGCTTGCATCCGCTGGTACATTGAGTTGGAGGACGGCTACTTGGTCGAGCAGGAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC