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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaggattagtaaaattcccctattttgagtagactccaatgcacaatatgtcaccgactcaaccactgcagactgacccttagttctacagatttacagGGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTAACAACACCAAGTACTATGAGGTTCTTGGAGTTCCTAAAACTGCAAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os04g46390.2
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|29678521|gb|CB674796.1|CB674796
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|29639999|gb|CB645008.1|CB645008
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|33694058|gb|CF322297.1|CF322297
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|218494200|gb|FG946885.1|FG946885
EST:     CCTCCGTCCG-CTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|29680639|gb|CB676914.1|CB676914
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|29678572|gb|CB674847.1|CB674847
EST:     CCTCCGCCCTCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|29643236|gb|CB648243.1|CB648243
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|29643291|gb|CB648298.1|CB648298
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|13807441|gb|AU181957.1|AU181957
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAG                         GGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTAA
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGgtacgatcgc ... agatttacagGGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTAA
EST: gi|29637040|gb|CB642049.1|CB642049
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|29668764|gb|CB665039.1|CB665039
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|14714017|gb|AU197958.1|AU197958
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|33657288|gb|CF279902.1|CF279902
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|29663531|gb|CB659806.1|CB659806
EST:     CCGCCTCGCCTCCACCGAGAGGTTCTCTC-GCCGTCGATTCGATTTACAG                         GGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTA
genomic: CCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----CGA-TT-CAGgtacgatcgc ... agatttacagGGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTA
EST: gi|29614042|gb|CB619055.1|CB619055
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|88352585|gb|CI624524.1|CI624524
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGATTTACAG                  
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCG-C----C-GA-TT-CAGgtacgatcgc ... aga
EST: gi|33657234|gb|CF279848.1|CF279848
EST:     CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAG                         GGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTAA
genomic: CCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGgtacgatcgc ... agatttacagGGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTAA

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: 74 (upstream exon), 75 (downstream exon)
Score: 22

CCTCTCTCGGTCGCGTGGCTTGAGCGGTGGTGACACCGCTCGCCTCCGTCCGCCTCGCCTCCACCGAGAGGTTCTCTCTGCCGCCGATTCAGgtacgatcgc ... agatttacagGGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTAACAACACCAAGTACTATGAGGTTCTTGGAGTTCCTAAAACTGCAAGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatgtcaccgactcaaccactgcagactgacccttagttctacagatttacagGGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTAACAACACCAAGTACTATGAGGTTCTTGGAGTTCCTAAAACTGCAAGCAAG
                          gactgac  putative branch site (score: 22)
                                             agattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaggattagtaaaattcccctattttgagtagactccaatgcacaatatgtcaccgactcaaccactgcagactgacccttagttctacagatttacagGGAGATTATCTTGTGATCTGTAAACATGTTTGGGCGTGTACCGAGGAGTAACAACACCAAGTACTATGAGGTTCTTGGAGTTCCTAAAACTGCAAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - agtaaaa
- - - - - - - - - - - - - - - - - - -caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgca