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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattagttatactgctgtagtgtatggaaatcagatggcttatgatgatttttttgtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC

Basic information

species Oryza sativa
transcript LOC_Os03g03920.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03920.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G057158_T01 (Zea mays), 3'ss of exon 4
gtaaattagttatactgctgtagtgt-atggaaatcagatggcttatgatgatttttttgtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC
|| | | | | |||||||| |||  | ||    |||| |     ||  ||| || | |  | || |  ||||||||| |||||||||||||| ||||||||||||||||| ||||||||| |||| | 
gtga-tcaatcatactgctctagcttcatatgcatcaaaaatacta-aatgtttctctcttttgca--gCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA

upper sequence: LOC_Os03g03920.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G127101_T01 (Zea mays), 3'ss of exon 4
gtaaattagttatactgctgtag-tgtatggaaatcagatggcttatgatgatttttttgtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC
|| | | | | |||||||| ||| |  |||   || | ||    || | || | ||| | |   |  |||||||||| || ||||||||||| ||||||||||||||||| |||||||||||||| | 
gtga-tcaatcatactgctctagatacatgtgcatgaaatatactaag-tgttctttcttt---tgcagCAATTAATTTCGTTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAGCTGGACA
















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|88844161|gb|CI001218.1|CI001218
EST:     CTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: CTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|29656527|gb|CB652802.1|CB652802
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|58588836|gb|CF987144.1|CF987144
EST:     TCCAGAACCCAGAATTTGTTCGCCAGCTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|88590511|gb|CI708279.1|CI708279
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|29662283|gb|CB658558.1|CB658558
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|88429036|gb|CI689915.1|CI689915
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|55436834|gb|CV731581.1|CV731581
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|88590503|gb|CI709368.1|CI709368
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|88582060|gb|CI699289.1|CI699289
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|29678486|gb|CB674761.1|CB674761
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|87007168|gb|CI277243.1|CI277243
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAGATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTA-ATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACA
EST: gi|218483111|gb|FG965896.1|FG965896
EST:     TCCAGAACCCAGAATTTGTTCGCCAGCTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|88588980|gb|CI706829.1|CI706829
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|29616126|gb|CB621138.1|CB621138
EST:     TCCAGAACCCAGAATTTGTTCGCCAGCTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|163919662|gb|EG711652.1|EG711652
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|29674370|gb|CB670645.1|CB670645
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|13420872|gb|AU174962.1|AU174962
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGC
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGC
EST: gi|86500583|gb|CI143216.1|CI143216
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|88591862|gb|CI709918.1|CI709918
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
EST: gi|86494120|gb|CI136753.1|CI136753
EST:     TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAG                         CAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA
genomic: TCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAA

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: 70 (upstream exon), 74 (downstream exon)
Score: 92

CCCAAATGTACGTAATATGATGGAATCTAACACTCAGTTGAGGGAGATGTTCCAGAACCCAGAATTTGTTCGCCAGTTGACATCTCCTGAAACTTTGCAGgtaaattagt ... gtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgctgtagtgtatggaaatcagatggcttatgatgatttttttgtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC
                                      tttttttgt  CT-rich tract
                             ttatgatgattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattagttatactgctgtagtgtatggaaatcagatggcttatgatgatttttttgtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG