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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgcaaataccctgacacgctggctgcatttcttagcccacaaaacatgaaagatgtattagtaaactgacaattggcatcatgggattagggg...

Basic information

species Oryza sativa
transcript LOC_Os03g55850.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55850.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G052423_T01 (Zea mays), 5'ss of exon 2
TGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgcaaataccctgacacgctggctgcatttcttagccc---acaaaacatgaaagatgtattagtaaactgacaattggcatcatgggattagggg
||||||||||  | || ||||||||||||||||||||||| ||||||||||| |||||||||||||| || ||||||  || |||||| |||||| | ||||   || ||| |||  ||    | |      || |    || |     ||   |||  |  |  | ||||| | |  |  || |   |||||  | || || 
TGATATTGGACCGCACGAACTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggcacataaactctatctcaattctcactgaccagtcttgtgcattgcatagatcaattgttagttacc--atgatagttttcatgtcactatgg-

upper sequence: LOC_Os03g55850.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G040030_T01 (Zea mays), 5'ss of exon 2
TGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgcaaat--accctgacacgctggctgcatttcttagcccacaaaacatgaaagatgtattagtaaac-tgacaattggcatcatgggattagggg-
||||||||||| | ||||| |||||||||||||||||||| ||||||||||| |||||||||||||| || ||||||  || |||||| |||||| | ||||   || ||  ||  |||||  | | ||  |  || | | | |     |    ||| |  |  | ||||| | | ||| | ||    |      ||  |  | 
TGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggcgcatcaaccctatctcacttac--caatccattgt--gtattgtatggatcaattgttagttaccatgatagtttttttgtcacaatgggcaga

upper sequence: LOC_Os03g55850.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv00s0207g00220.t01 (Vitis vinifera), 5'ss of exon 2
TGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtat-atatgcaaataccctgacacgctggctgcatttcttagcccacaaaacatgaaagatgtattagtaaactgacaattggcatcatgggattagggg
||||| ||||| ||||||||||||  ||||||||||||||  | || ||||| ||||||||||||||||  || |||  ||   |||||    | ||||||| | || |   | |   |  ||||  |   |   |||  |    |  | | | |   |   | | || |    | |   |                    
TGATACTGGATCGGACAAACTGGAGAACCAACATGCTGACTTCGCTTTTGGTTCCTTACATTTTCTTTAGTCTTCCTCCTGTATTGTTCAACTTATTGAGgtttcatcttttactgatcgcacacttttattctcttttatttttctgatatcttattaatagaactaattttattatggtccag----------------

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|29656136|gb|CB652411.1|CB652411
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|218505408|gb|FG953377.1|FG953377
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|119002221|gb|CU234192.1|CU234192
EST:     TTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: TTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|88825479|gb|CI776044.1|CI776044
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTT
EST: gi|29667854|gb|CB664129.1|CB664129
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|58591798|gb|CF990106.1|CF990106
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|86494252|gb|CI136885.1|CI136885
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|88835395|gb|CI005085.1|CI005085
EST:     TTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: TTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|29667853|gb|CB664128.1|CB664128
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|58591068|gb|CF989376.1|CF989376
EST:     GTCCCTTACATTTTCTTTACACTGCCTGATGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|38473864|gb|CF957996.1|CF957996
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|29626644|gb|CB631655.1|CB631655
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|568835|gb|D39684.1|D39684
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCAATCATTGCTTGTCATCCTTCGTCTCT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCT-GTCATCCTTCGTCTCT
EST: gi|58586796|gb|CF985104.1|CF985104
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|66913495|gb|CX100343.1|CX100343
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|88736312|gb|CI759820.1|CI759820
EST:     GTCCCTTACATTTTCTTTACACTGCCTGCTGGGCTGTTCTCTCTGTCGAG                         GGGAGAAATCGGAAAATGGAT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGAT
EST: gi|88201754|gb|CI202109.1|CI202109
EST:     GGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|86496839|gb|CI139472.1|CI139472
EST:     ACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: ACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|29626645|gb|CB631656.1|CB631656
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|218480554|gb|FG955808.1|FG955808
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
EST: gi|88407922|gb|CI588951.1|CI588951
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAACTGGATTGCGATCATTGCTGTAATCC
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCC
EST: gi|38480635|gb|CF964724.1|CF964724
EST:     GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAG                         GGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT
genomic: GTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTT

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: 61 (upstream exon), 71 (downstream exon)
Score: 37

TGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgc ... taaattgcagGGGAGAAATTGGAAAATGGATTGCGATCATTGCTGTCATCCTTCGTCTCTTCTTTCCTCGCCATTTCCCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCTCTGTTGAGgtatatatgcaaataccctgacacgctggctgcatttcttagcccacaaaacatgaaagatgtattagtaaactgacaattggcatcatgggattagggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgctggc