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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taactatatatgcttgtagtttactgctgtctatttaattgtttttccacatggcttctctaattacctttttttgtgcatgttttctgtcttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACTTCAGCACCACAATCTGATCTTGGCATTGAT

Basic information

species Zea mays
transcript GRMZM2G062953_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062953_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 8
taactatatatgcttgtagtttactgctgtctatttaattgt--ttttccacatggcttctctaattacctttttttgtgcatgttttctgtctt-gtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACTTCAGCACCACAATCTGATCTTGGCATTGAT
| |  || |||  | |||  ||  |  | | |  ||| || |  | ||  || |||||||| |||| || | | ||||  |||||   ||| ||| |||||||| | ||||  || || || ||||||||| |||| ||||||||||| || |||||||||||| |||||||  |||||||| |||| ||||||||| | |||
tgatgatctatattcgtaactttttttt-tttgattatttatcatgttttacctggcttctttaataacatctgtttg--catgtgacctgcctttgtaacagTGCCAGTGTGCAGTCACCATTTGAGCAACTAGCGCTTCCAGCACCTCCGGTGTCAAATGGCTCAGCAACCCCAGCACCAAAATCCGATCTTGGCGTCGAT
















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|22490527|gb|BU050450.1|BU050450
EST:     GATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAG                         TACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
genomic: GATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAGgtttgcttcc ... cttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
EST: gi|20300238|gb|BQ163181.1|BQ163181
EST:     GATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAG                         TACAAGTGACCAATCTCCTTNTGAGCAATTAGCTCTTCCAGCACCACCAGN
genomic: GATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAGgtttgcttcc ... cttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
EST: gi|87153881|gb|DY398670.1|DY398670
EST:     GATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAG                         TACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
genomic: GATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAGgtttgcttcc ... cttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
EST: gi|71438882|gb|DR819932.1|DR819932
EST:     GATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAG                         TACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT
genomic: GATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAGgtttgcttcc ... cttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGT

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: 47 (upstream exon), 46 (downstream exon)
Score: 148

AGACCAAGGATTCGACAAACCAGGATTCCAAAAAGGAGCAAGGACTCATAGATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAGgtttgcttcc ... cttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACTTCAGCACCACAATCTGATCTTGGCATTGAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 427

AGACCAAGGATTCGACAAACCAGGATTCCAAAAAGGAGCAAGGACTCATAGATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAGgtttgcttcc ... cttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACTTCAGCACCACAATCTGATCTTGGCATTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 466

AGACCAAGGATTCGACAAACCAGGATTCCAAAAAGGAGCAAGGACTCATAGATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAGgtttgcttcc ... cttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACTTCAGCACCACAATCTGATCTTGGCATTGAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 333

AGACCAAGGATTCGACAAACCAGGATTCCAAAAAGGAGCAAGGACTCATAGATATTGAGGATCCCACAAGTCAAGATGCTGCAAAAGATCCAAATCAAAGgtttgcttcc ... cttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACTTCAGCACCACAATCTGATCTTGGCATTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacatggcttctctaattacctttttttgtgcatgttttctgtcttgtaacagTACAAGTGACCAATCTCCTTTTGAGCAATTAGCTCTTCCAGCACCACCAGTGTCAAATGGCGCAGCAACTTCAGCACCACAATCTGATCTTGGCATTGAT
            ctctaat  putative branch site (score: 333)
                                     ttttctgtctt  putative PPT
               taattaccttttttt  TA-rich tract