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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTCAGGATGCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagctagctcatgtacattttactggaacatttgttttgcagttcagtcccttatagactagtgccgctgacttttaagttatgtgcataaagc...

Basic information

species Oryza sativa
transcript LOC_Os11g41900.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g41900.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G878139_T02 (Zea mays), 5'ss of exon 3
CGCTCAGGATGCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagctagctcatgtacattttactggaacattt-gttttgcagttcagtcccttatagactagtgccgctgacttttaagttatgtg-cataaagc-
|||||||| |||||||||||||| || ||||| |||||||| ||||| || |||||||||||||||||  ||| |||| |  || || ||| ||||| | ||||| || ||||    |  || |   ||| |   |  |     | ||| |   ||||||   
CGCTCAGGGTGCCTTGGAAGTACGCTCGCTGTCATGAAGAAGTCATCCAAGTTCCTTCCAgtgagtta-ttagttcatatgtatatttctgtaacatgtagttttacaattcatatgcacattgg--agttctatttgcagcataattaagcaacataaacaa

upper sequence: LOC_Os11g41900.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G037104_T02 (Zea mays), 5'ss of exon 4
CGCTCAGGATGCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagctagctcatgtacattttactggaacattt-gttttgcagttcagtcccttatagactagtgccgctgacttttaagtta-tgtgcataaagc----
|| ||||| ||||||||||||||||||||||| |||||||| ||||| || |||||||||||||||||| |    ||| |  || || ||| ||||| | | ||| || || |    |  ||     ||| | | ||| ||| | ||   | |  |||||      
CGTTCAGGGTGCCTTGGAAGTACACTTGCTGTCATGAAGAAGTCATCCAAGTTCCTTCCAgtgagttagtt----catatgtatatttctgtaacatgtagctttacaatttatatgcacatcag--agttctgttgattttaatgtaggttttaataaaaactat

upper sequence: LOC_Os11g41900.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G31320.1 (Glycine max), 5'ss of exon 5
CGCTCAGGATGCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagctagctcatgtacatttt--actggaacatttgttttgcagttcagtcccttatagactagtgccgctgacttttaagttatgtgcataaagc--
|| ||||| |||||||| || ||||||||||| ||||||||||| || || || || || ||  |||   |     ||  |  ||||  | || || | | |  |  || ||  ||     |   | || |     | |   ||   | | |   ||  |    
CGTTCAGGTTGCCTTGGCAGCACACTTGCTGTGATGAAGAAATCTTCAAAGTTTCTACCGgtatgttttgttagaaattgatgttttgaaatgaaaaaatggaatgacattt--gttttccaatcattattatt--taatggtttgatcagggtgatggaaata

upper sequence: LOC_Os11g41900.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G12560.1 (Glycine max), 5'ss of exon 5
CGCTCAGGATGCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagtta-gctagctcatgtacattttac-tggaacatttgttttgcagtt-----cagtcccttatagactagtgccgctgacttttaagttatgtgcataaagc
|| ||||| |||||||| || || |||||||| ||||||||||||||||| || || || ||  |||  | |||    |||   ||| |  || ||   | |  | ||| ||     |  | | ||||    || ||  | |   |     || |||   ||     
CGTTCAGGTTGCCTTGGCAGCACTCTTGCTGTGATGAAGAAATCATCGAAGTTTCTACCGgtatgttttgttagaaattgttgttttaaaatgaaaagatggaatggcatttgctttccattcattatgatttaatg--gtttgatcaggggtgatggaaat-----

upper sequence: LOC_Os11g41900.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 5'ss of exon 5
CGCTCAGGATGCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagctagctcatgtacattttactggaacatttgttttgcagttcagtcccttatagactagtgccg--ctgacttttaagttatgtgcataaagc---
|| ||||| |||||||| || ||| | ||||| |||||||||||||| ||||||||||| || ||||    |||| |  |    | | ||| ||   |  ||   || |  || | |||   |   |  |      | |  |        | |   | ||||   
CGATCAGGTTGCCTTGGCAGCACATTAGCTGTAATGAAGAAATCATCAAAATTCCTTCCGgtaagtttctaagctgacatg---tgtgctgtaaatgtcattc--caatgaagcctcttgatgctaaaggttaaatttagctcgtgtccttattagtgaagctac

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|29658270|gb|CB654545.1|CB654545
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|58680428|gb|CK069115.1|CK069115
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACC
EST: gi|88263764|gb|CI366665.1|CI366665
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|117217204|gb|CT845404.1|CT845404
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|29639076|gb|CB644085.1|CB644085
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|29680413|gb|CB676688.1|CB676688
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|58683813|gb|CK072500.1|CK072500
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|29639118|gb|CB644127.1|CB644127
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|112785295|gb|EE590405.1|EE590405
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|29615789|gb|CB620801.1|CB620801
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|58601667|gb|CK012195.1|CK012195
EST:     CACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: CACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|4714815|gb|AU055932.1|AU055932
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|58669640|gb|CK058326.1|CK058326
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
EST: gi|29686573|gb|CB682848.1|CB682848
EST:     GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCA                         GTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGC

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), 73 (downstream exon)
Score: 52

CGCTCAGGATGCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagc ... cattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGCTGGGCAAAGGATGAAAAGACATTGAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTCAGGATGCCTTGGAAGTACACTTGCTGTTATGAAGAAATCATCGAAATTCCTTCCAgtgagttagctagctcatgtacattttactggaacatttgttttgcagttcagtcccttatagactagtgccgctgacttttaagttatgtgcataaagc

- - - - - - - TGGAAG
- - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgctg