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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcttgtactgcaattagttccattatttttacctgtttagtagcatatttaaggcgattctgtggtgactgttctgaacatttcattcattgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTAACAAAGGGTCAAGAACTCACTGTTACCACCGATTATGAGATCAAGGGTG

Basic information

species Oryza sativa
transcript LOC_Os04g58110.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008714_T01 (Zea mays), 3'ss of exon 1
-----cttcttgtactgcaattagttccattatttttacctgtttagtagcatatttaaggcgattctgtggtgactgttctgaacatttcattcattgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTAACAAAGGGTCAAGAACTCACTGTTACCACCGATTATGAGATCAAGGGTG
          |||   ||||  | |||     || |||     || |||  | |||||||| |   || |  | | |||||| ||    |  ||  | ||| |||||||||||||| ||||| || |||||||||||||| || || || |||||||| |||||||||||| ||||||| ||||| |||||||| ||||||||||
taagtagctatgtgtagcaaa-aattctgactttattatt--ctttgtatgacatttaaggtgg--ctatattaagtgttcttaatcagttttttgtggctgcagGGTCCTGAGATCCGTACAGGGTTTTTGAAGGATGGTAAACCGATTAAGCTAACCAAGGGTCAAGAAATCACTGTCACCACTGATTATGATATCAAGGGTG

upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 1
----cttcttgtactgcaattagttccattatttttacctgtttagtagcatatttaaggcgattctgtggtgactgttctgaacatttcattcattgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTAACAAAGGGTCAAGAACTCACTGTTACCACCGATTATGAGATCAAGGGTG
      | || |   ||||  | |||  | | | |   ||  || |||| | ||||||||   ||   ||   | |||||| |     || ||  || || |||||||||||||||||||| || |||||||||||||| || ||||| |||||||| |||||||||||  ||||||||||||| |||||||| ||||||||||
ccatgatattatgtagcaaaaaattc--tgactgtgttcttctttgtaggacatttaaggttgttgcatg--aagtgttcttagtcagtcttttgtttctgcagGGTCCTGAGATTCGTACAGGGTTTTTGAAGGATGGTAAACCAATTAAGCTAACCAAGGGTCAAGAGATCACTGTTACCACTGATTATGATATCAAGGGTG
















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|33685156|gb|CF313395.1|CF313395
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|33795678|gb|CF323709.1|CF323709
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|58690506|gb|CK079193.1|CK079193
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GTGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCT
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagG-GTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCT
EST: gi|29614582|gb|CB619595.1|CB619595
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|29662435|gb|CB658710.1|CB658710
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|27576608|gb|CA999302.1|CA999302
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|58606356|gb|CK034389.1|CK034389
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|29619331|gb|CB624343.1|CB624343
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|58609916|gb|CK037949.1|CK037949
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGG
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGG
EST: gi|58671553|gb|CK060239.1|CK060239
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|29614496|gb|CB619509.1|CB619509
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|33678847|gb|CF307086.1|CF307086
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|58608755|gb|CK036788.1|CK036788
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|58663680|gb|CK052366.1|CK052366
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|5003739|gb|AU068888.1|AU068888
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAN                         GGTCCTGAGATTCGTACTGGATTTTTGAAAGATTGCAAGCCAATCAAG-TA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|569547|gb|D40396.1|D40396
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTNNAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|29676064|gb|CB672339.1|CB672339
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|29616704|gb|CB621716.1|CB621716
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|33797184|gb|CF324456.1|CF324456
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|300216331|gb|HO088116.1|HO088116
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|569585|gb|D40434.1|D40434
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|58607601|gb|CK035634.1|CK035634
EST:     AGGCCATGCACAACACCGGCGTTCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
EST: gi|33690020|gb|CF318259.1|CF318259
EST:     AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAG                         GGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA
genomic: AGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTA

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: 75 (upstream exon), 72 (downstream exon)
Score: 268

CTCCCACGGCACCCACGAGTACCACCAGGAGACCCTCGACAACCTCCGCCAGGCCATGCACAACACCGGCGTCCTCTGCGCCGTCATGCTCGATACCAAGgttaccccct ... attgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTAACAAAGGGTCAAGAACTCACTGTTACCACCGATTATGAGATCAAGGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatttaaggcgattctgtggtgactgttctgaacatttcattcattgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTAACAAAGGGTCAAGAACTCACTGTTACCACCGATTATGAGATCAAGGGTG
                                              ttgcttc  CT-rich tract
                                    atttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcttgtactgcaattagttccattatttttacctgtttagtagcatatttaaggcgattctgtggtgactgttctgaacatttcattcattgcttcagGGTCCTGAGATTCGTACTGGATTTTTGAAGGATGGCAAGCCAATCAAGCTAACAAAGGGTCAAGAACTCACTGTTACCACCGATTATGAGATCAAGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
cttcttg
- - - -tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaaca