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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatattgcaataggataagttgtaacgcagtttatcctcacttggatacgtttccacaggttacattactgatgtgtctcgtgaacttttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGGGTTTATGCATGACAGCCCCTGCAGTCCTTCCAAATGAGTTAGAAGGGAT

Basic information

species Oryza sativa
transcript LOC_Os02g57660.1
intron # 1
splice site 3'
intron type U2

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|88723551|gb|CI747061.1|CI747061
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88313018|gb|CI592302.1|CI592302
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTACTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88336854|gb|CI626934.1|CI626934
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88695413|gb|CI737916.1|CI737916
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88403248|gb|CI570989.1|CI570989
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88412816|gb|CI576080.1|CI576080
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88352184|gb|CI613835.1|CI613835
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTC-TAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88317267|gb|CI626910.1|CI626910
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88413332|gb|CI581347.1|CI581347
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88741890|gb|CI764395.1|CI764395
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88718434|gb|CI741944.1|CI741944
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTC
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTC
EST: gi|88730771|gb|CI754384.1|CI754384
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88298956|gb|CI567959.1|CI567959
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACCTGTGGGTTAGTC-TCCTAGTG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGAC-TGTGGGTTAGTCCTCCTAGTG
EST: gi|88718054|gb|CI741564.1|CI741564
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGAATGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88724291|gb|CI747550.1|CI747550
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCNCCCTGG                         GCCGTGCTTAGGAGTATCTTCCCTCGCGAATGTGGGTTAGTCCTCCTAGTG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCC-TCGCGACTGTGGGTTAGTCCTCCTAGTG
EST: gi|88724145|gb|CI749155.1|CI749155
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCT
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCT
EST: gi|88723285|gb|CI746795.1|CI746795
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTG
EST: gi|88743243|gb|CI766751.1|CI766751
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88357069|gb|CI615956.1|CI615956
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGAGTGTGGGTTAGTCCTCCTAGCTG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAG-TG
EST: gi|88385952|gb|CI568620.1|CI568620
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88695521|gb|CI737559.1|CI737559
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTANGAGTATCTTCCTCGCGANTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88298842|gb|CI566039.1|CI566039
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88367742|gb|CI570481.1|CI570481
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88760304|gb|CI769860.1|CI769860
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
EST: gi|88361384|gb|CI626488.1|CI626488
EST:     CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGG                         GCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG
genomic: CGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGG

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: 59 (upstream exon), 33 (downstream exon)
Score: 5

GGGATTCCCTCCAGATCGCCATTCGATTCGCTGCTGCTGCTCCGCCTCGTCGTCGCCGTCGTCGAGTTCGTCTCGCAATCGCCTCCTCCTCTCCCCCTGGgtacgtacca ... ttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGGGTTTATGCATGACAGCCCCTGCAGTCCTTCCAAATGAGTTAGAAGGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatacgtttccacaggttacattactgatgtgtctcgtgaacttttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGGGTTTATGCATGACAGCCCCTGCAGTCCTTCCAAATGAGTTAGAAGGGAT
                       tactgat  putative branch site (score: 5)
                                          cttttctttac  putative PPT
                                           ttttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatattgcaataggataagttgtaacgcagtttatcctcacttggatacgtttccacaggttacattactgatgtgtctcgtgaacttttctttacagGCCGTGCTTAGGAGTATCTTCCTCGCGACTGTGGGTTAGTCCTCCTAGTGGGTTTATGCATGACAGCCCCTGCAGTCCTTCCAAATGAGTTAGAAGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - tattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgt