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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcttccatcactgttgcatatgctcttaataactctcataatgtctacaaatatgttaatacattcatatgtaatttaattgttttccagatgacttctctaattactttcttttatgcatgttatctttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACAAAATCTGACCTTGGCATTGATCTTCTGAGC

Basic information

species Zea mays
transcript GRMZM2G153138_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 8
gtttgcttccatcactgttgcatatgctcttaataactctcataatgtctacaaatatgttaatacattcatatgtaatttaattgttttccagatgacttctctaattactttcttttatgcatg--ttatctttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAAC---------AAAATCTGACCTTGGCATTGATCTTCTGAGC
                                          | |||     | ||  || | |   ||  | ||    || ||  | ||  |  || ||||| |||| || |   |||     ||   |  |||||||||||| | ||||  || || || ||||||||| |||| ||||||||||| || |||||||||||| |||||||         |||||| || |||||| | |||         
------------------------------------------tgatgatc-tatattcgtaactttttttttttgattatttatcatgttttacctggcttctttaataacatctgtttgcatgtgacctgcctttgtaacagTGCCAGTGTGCAGTCACCATTTGAGCAACTAGCGCTTCCAGCACCTCCGGTGTCAAATGGCTCAGCAACCCCAGCACCAAAATCCGATCTTGGCGTCGAT---------
















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|71441431|gb|DR822481.1|DR822481
EST:     GATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAG                         TACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
genomic: GATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAGgtttgcttcc ... tttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
EST: gi|78089227|gb|DV517601.1|DV517601
EST:     GATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAG                         TACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
genomic: GATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAGgtttgcttcc ... tttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
EST: gi|18655222|gb|BM500027.1|BM500027
EST:     GATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAG                         TACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
genomic: GATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAGgtttgcttcc ... tttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
EST: gi|87152145|gb|DY396934.1|DY396934
EST:     GATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAG                         TACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
genomic: GATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAGgtttgcttcc ... tttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT

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), 48 (downstream exon)
Score: 287

AGACTGAGGATTCGGCAAACCAGGACTCCAAAAAGGAGCAGGGACTCATAGATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAGgtttgcttcc ... tttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACAAAATCTGACCTTGGCATTGATCTTCTGAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 826

AGACTGAGGATTCGGCAAACCAGGACTCCAAAAAGGAGCAGGGACTCATAGATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAGgtttgcttcc ... tttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACAAAATCTGACCTTGGCATTGATCTTCTGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 607

AGACTGAGGATTCGGCAAACCAGGACTCCAAAAAGGAGCAGGGACTCATAGATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAGgtttgcttcc ... tttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACAAAATCTGACCTTGGCATTGATCTTCTGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 940

AGACTGAGGATTCGGCAAACCAGGACTCCAAAAAGGAGCAGGGACTCATAGATATTGAGGATCCCACAAGCCAAGATGCTGCAAAAGAGCCAAATCAAAGgtttgcttcc ... tttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACAAAATCTGACCTTGGCATTGATCTTCTGAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccagatgacttctctaattactttcttttatgcatgttatctttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACAAAATCTGACCTTGGCATTGATCTTCTGAGC
               ctctaat  putative branch site (score: 940)
                                        ttatcttt  putative PPT
                  taattactttctttta  TA-rich tract