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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAGATGGCAGACTGAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatcctgggaaatgatttggcttttttttggctttaggacatgttaatctttgtcagatatccttctcattatcttcttctatttgacttcatg...

Basic information

species Oryza sativa
transcript LOC_Os03g61050.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61050.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA03G14690.1 (Glycine max), 5'ss of exon 2
CTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAGATGGCAGACTGAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatcctgggaaatgatttggcttttttttggctttaggacatgttaatctttgtcagatatccttctcattatcttcttctatttgacttcatg
|  |  ||||  | ||||| || ||  || | ||||| |||||||| || ||||||||||||||||| ||||||| ||| ||||| |||||||| ||||||||   |    || |   || |||     |  ||||  |||  |  || || || |||||   || ||   ||  || | ||                  
CACTTGTGAATTCAAAGTGCCCCAAGAATTTGGAGCTCAGATGGCAAACAGAAGTTAGTTCCAGCATCTATGCAAATCCCTTGATTGCTGATATTAACAGgta---ttgtttgtgctttgctttttgagtgatttgtgtttgtgtgattttcat-tttgttgaatgtctgcctttttgttttgcag--------------

upper sequence: LOC_Os03g61050.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA01G27250.1 (Glycine max), 5'ss of exon 2
CTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAGATGGCAGACTGAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatcc-tgggaaatgatttggcttttttttggctttaggacatgttaatctttgtcagatatccttctcattatcttcttctatttgacttcatg
|  |  ||||  | |||||||| ||  || | |||||  ||||||| || ||||||||||||||||| |||||||  || ||||| |||||||| |||||||||  | |   || |   || |||     |  ||||  |||  |  || || || |||||   || ||   ||  || | ||                  
CACTTGTGAATTCGAAGTGTCCCAAGAATTTGGAGCTCCGATGGCAAACAGAAGTTAGTTCCAGCATCTATGCAAACCCCTTGATTGCTGATATTAACAGgtaagttgtttatgtgctttgctttttgagtgatttgtgtttgtgtaattttcat-tttgttgaatgtctgcctttttgttttgcag--------------

upper sequence: LOC_Os03g61050.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 5'ss of exon 2
CTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAGATGGCAGACTGAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaata-----tcctgggaa--atgatttggcttttttttggctttaggacatgttaatctttgtcagatatcct-tctcattatcttcttctatttgacttcatg----------------
|||| || || ||   ||| ||   | || | ||| ||||||||||||| || ||||| || ||||| ||||| || || |||||||||||||| ||||||| | | |      ||| |  |  || || |  || |    |  | ||      || |    || |      ||| | | |  |||  || |  |||  | | |                    
CTTTGTTAAATACACGGTGCCCTCGAAATTTGGAGTTGAGATGGCAGACAGAGGTTAGCTCTAGCATATATGCTACCCCATTGATCGCTGATATTAACAGgtgagaaaaatcccccttgttactattatctaactatgagcttcccttgatcattgattcatttggcataggatcttatattcttagattttgatatggggcctttctatgttttgtttctcag

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|88344836|gb|CI624487.1|CI624487
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88390343|gb|CI607379.1|CI607379
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAA
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAA
EST: gi|88396364|gb|CI598476.1|CI598476
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATC
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATC
EST: gi|58607225|gb|CK035258.1|CK035258
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88407008|gb|CI578536.1|CI578536
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCAT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCAT
EST: gi|88395082|gb|CI609398.1|CI609398
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88431688|gb|CI576879.1|CI576879
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGA
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGA
EST: gi|88423838|gb|CI609869.1|CI609869
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88324539|gb|CI568158.1|CI568158
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTG
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTG
EST: gi|58672499|gb|CK061185.1|CK061185
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88426667|gb|CI579496.1|CI579496
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGT
EST: gi|88316701|gb|CI624143.1|CI624143
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGG
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGG
EST: gi|88388791|gb|CI592679.1|CI592679
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGC-ATCATTTGTTCAT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCAT
EST: gi|88396846|gb|CI577995.1|CI577995
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|13447553|gb|AU181047.1|AU181047
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88422933|gb|CI615233.1|CI615233
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|7378442|gb|AU088713.1|AU088713
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88363740|gb|CI609097.1|CI609097
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88390242|gb|CI605695.1|CI605695
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATC
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATC
EST: gi|88362332|gb|CI608723.1|CI608723
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88350368|gb|CI623306.1|CI623306
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTA
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTA
EST: gi|88359727|gb|CI622417.1|CI622417
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTA
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTA
EST: gi|5607636|gb|AU076308.1|AU076308
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGT
EST: gi|88417906|gb|CI596583.1|CI596583
EST:     GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAG                         CGATGGAAAGTTGGAAGTAGTGGTG
genomic: GAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTG

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: 66 (upstream exon), 65 (downstream exon)
Score: 21

CTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAGATGGCAGACTGAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatc ... ggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGTTCTTGAAGGCTCTGATGGGGACAAATTGCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAGATGGCAGACTGAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCTGATATCAACAGgtaaaatatcctgggaaatgatttggcttttttttggctttaggacatgttaatctttgtcagatatccttctcattatcttcttctatttgacttcatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT