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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGATGGGATTATCCTTCGCAATCATATTTCACGAATCCTTCAACGCCACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatatcttctgacataataatttattcatgctacatgtactgaatgcttcttgcatacgaccgatccacttttttatgttttcag

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 4
AAATGATGGGATTATCCTTCGCAATCATATTTCACGAATCCTTCAACGCCACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaa-tcatatcttctgacataataatttattcatgctacatgtactgaatgcttcttgcatacgaccgatc-cacttttttatgttttcag
||||||||| |||||||||||||| |||||||||||||| ||||||||||| || || || ||||  |||||||||||| | |||||  | ||||||||||||| |  |||||||||||||    || |  |   |  | |  ||||| | ||||||  |  | | ||  |   |  ||||| | || | ||
AAATGATGGTATTATCCTTCGCAACCATATTTCACGAATTCTTCAACGCCATTTTAAAGGAAAGCTGTATTATGTTGATCTCATTGATTTGTTCAATGAGgtaagttgtatcttctgacatgcacatattgttgggaaaaaaatactgtacgcttctccctgatgcccagttgtatgtttttgttttgttag
















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|148972761|gb|EE023734.2|EE023734
EST:     ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|149102315|gb|EE188183.2|EE188183
EST:     ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|149081093|gb|EE170194.2|EE170194
EST:     ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|148986685|gb|EE030467.2|EE030467
EST:     ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|71437045|gb|DR818095.1|DR818095
EST:     ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|148942982|gb|EC888030.2|EC888030
EST:     ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAG                         GTTGAGTTCAAGACAGCTTCCGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|148943253|gb|EC888314.2|EC888314
EST:     ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|74235474|gb|DT643388.1|DT643388
EST:     ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC

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: 49 (upstream exon), 47 (downstream exon)
Score: 38

AAATGATGGGATTATCCTTCGCAATCATATTTCACGAATCCTTCAACGCCACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 52

AAATGATGGGATTATCCTTCGCAATCATATTTCACGAATCCTTCAACGCCACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 25

AAATGATGGGATTATCCTTCGCAATCATATTTCACGAATCCTTCAACGCCACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

AAATGATGGGATTATCCTTCGCAATCATATTTCACGAATCCTTCAACGCCACTTCAAGGGGAAGCCATATTATGTTGATGTAATTGACCTATTCAATGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT