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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatatttagtttcgtcgagcaaactttcagtataaacatagtgcatcaaaattaatgtcggtgctttcttgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA

Basic information

species Zea mays
transcript GRMZM2G103047_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103047_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 3'ss of exon 2
gtga--atattt-------agtttcgtcgagcaaactttcagtataaacatagtgcatca--aaattaatgtcggtgctttcttgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA
|| |  ||||||       || | | ||| |  ||| |||  || | |  || ||||  |  ||   ||     ||   |     | |  ||||||  ||||||||||||||| ||||| || || |||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||
gtaattatatttctctataagatacatcgtgacaacattcgatacacatgtattgcactatgaagccaactattgtaactgtccttatttcagCTTGCTGCTATCCTTCCTCTCGCTATGGTCCACACCATGGGCAATCTTTTCACGAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATCA

upper sequence: GRMZM2G103047_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27053 (Selaginella moellendorffii), 3'ss of exon 2
gtgaatatttagtttcgtcgagcaaactttcagt-ataaacatagtgcatca-aaattaatgtcggtgctttcttgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA
           || ||||||   ||| | ||  |  |    || | |||||  ||| |  ||||  || ||  | ||     || |  | || ||| | || || ||  | || || |||||||| ||||| || || ||||||||||||||||||||||||||||| ||||| || || ||||
-----------gtatcgtcgtagaaattgtcgtttgtgtcgatcgagcatctcaaacttttgtccttgtttcttcgt-----agGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCGTTTACTCACACAATCA

upper sequence: GRMZM2G103047_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 2
gtgaatatttagtttcgtcgagcaaactttcagt-ataaacatagtgcatcaaaattaatgtcggtgctttcttgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA
           || ||||||   ||| | ||  |  |  | || | |||||   |  ||| | |   | || ||  |||  || |  | || ||| | || || ||  | || || |||||||| ||||| || || ||||||||||||||||||||||||||||||||||| || || ||||
-----------gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttg--tccttgtttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA

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|148999234|gb|EE036154.2|EE036154
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|211274928|gb|FL373271.1|FL373271
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCT
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCT
EST: gi|71427134|gb|DR808184.1|DR808184
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|60349997|gb|DN216970.1|DN216970
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|21760182|gb|BQ635723.1|BQ635723
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGAGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|78125801|gb|DV544185.1|DV544185
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCA
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCA
EST: gi|76916104|gb|DV166241.1|DV166241
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|211501651|gb|FL380183.1|FL380183
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCA
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCA
EST: gi|211254579|gb|FL410492.1|FL410492
EST:     TTATGTGGATCACCGGTATCCTTAAAGGGC-AAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|74235578|gb|DT643492.1|DT643492
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|211047986|gb|FL382472.1|FL382472
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|9794211|gb|BE552519.1|BE552519
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|211330230|gb|FL404919.1|FL404919
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|50331502|gb|CO526628.1|CO526628
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|78082339|gb|DV510751.1|DV510751
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|149105847|gb|EE291446.2|EE291446
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|149072472|gb|EE160748.2|EE160748
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|76018097|gb|DT945267.1|DT945267
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|149070713|gb|EE159128.2|EE159128
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|71444331|gb|DR825381.1|DR825381
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|211069261|gb|FL419934.1|FL419934
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATC
EST: gi|149094831|gb|EE180400.2|EE180400
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|211476303|gb|FL383240.1|FL383240
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTAT
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTAT
EST: gi|78078232|gb|DV506647.1|DV506647
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|26457500|gb|CA829083.1|CA829083
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|4753301|gb|AI657206.1|AI657206
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|31358649|gb|CD443006.1|CD443006
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|78121642|gb|DV540026.1|DV540026
EST:     TATGTGGATCACCGGTATCCTTAAA-GGCCAAAGATTTCTGGGTGCC-AG                         CTTTTTGCTATCCTTCCTCTAGCTATTCGT-CATACCA
genomic: TATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGG-TGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTAT-CGTTCATACCA
EST: gi|50334494|gb|CO529620.1|CO529620
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|149007367|gb|EE040217.2|EE040217
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|211071293|gb|FL399387.1|FL399387
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTC
EST: gi|211063599|gb|FL411764.1|FL411764
EST:     TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAG                         CTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGG
genomic: TTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGG

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 347

TATAAACATCACCACAGTGCAGTTTGCCGTTGGAAGTGCCATTGCTTTGTTTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

TATAAACATCACCACAGTGCAGTTTGCCGTTGGAAGTGCCATTGCTTTGTTTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 449

TATAAACATCACCACAGTGCAGTTTGCCGTTGGAAGTGCCATTGCTTTGTTTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 575

TATAAACATCACCACAGTGCAGTTTGCCGTTGGAAGTGCCATTGCTTTGTTTATGTGGATCACCGGTATCCTTAAAAGGCCAAAGATTTCTGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagtataaacatagtgcatcaaaattaatgtcggtgctttcttgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA
                         aattaat  putative branch site (score: 575)
                                     tgctttcttgtttccc  putative PPT
                    atcaaaattaatgt  TA-rich tract