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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaaggtcatgtgtgccatgcagtacacaaattgttggtgtcttgtatgtccaatgcacttatctgatcatgaaaactacacttcacctgcgaatactttattagcttaaatgcttatttcatccacaaatccctttagtaaattagtcaaatatttaaaattctttgtttaatag

Basic information

species Zea mays
transcript GRMZM2G088397_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088397_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g45390.2 (Oryza sativa), 5'ss of exon 3
GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaaggtcatgtgtgccatgcagtacacaaattgttggtgtcttgtatgtccaatgcacttatctgatcatgaaa-actacacttcacctgcgaatactttattagcttaaat----gcttatttcatccacaaatccc----tttagtaaattagtcaaatatttaaaattct-------ttgtttaatag
 || |||||||||||||| |||||||||||||| ||||||| | ||| |       |  || || ||    |  ||  |  | | |||||||       ||||| | |||| ||     | | ||||||| |||| |||| ||||| | | | | |    |  | | | |||   |  | ||    |||  ||   |  |   ||||| |   || |       |||||| | ||
ATGCATCAAAATTGCTATCGTGCATGACATTGCTGAAGgtatgccaaagaacaccctatca-gctgtttttagcttaattttctattgtatg-------cacttgt-tgataatatgttattgcacttcatctgccaata-tttatcatccttattctaggactgtataatctgtatgttcccacttttcttagcatccttttatattcaggtttttatcctttttgtttgacag
















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|26557485|gb|CA829720.1|CA829720
EST:     GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG                         CTATTGTTGGTGACATTACCCCATCGGA
genomic: GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaag ... tgtttaatagCTATTGTTGGTGACATTACCCCATCGGA
EST: gi|32840843|gb|CD980524.1|CD980524
EST:     GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG                         CTATTGTTGGTGACATTACCCCATCGGATGGTATACCTAAGGCTGAAAAAA
genomic: GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaag ... tgtttaatagCTATTGTTGGTGACATTACCCCATCGGATGGTATACCTAAGGCTGAAAAAA
EST: gi|194717181|gb|FK934334.1|FK934334
EST:     GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG                         CTATTGTTGGTGACATTACCCCATCGGATGGTATACCTAAGGCTGNNNNNN
genomic: GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaag ... tgtttaatagCTATTGTTGGTGACATTACCCCATCGGATGGTATACCTAAGGCTG-AAAAA

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: 37 (upstream exon), 49 (downstream exon)
Score: 137

GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaag ... tgtttaatagCTATTGTTGGTGACATTACCCCATCGGATGGTATACCTAAGGCTGAAAAAAGCCGGCGCGAACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGG


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 55

GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaag ... tgtttaatagCTATTGTTGGTGACATTACCCCATCGGATGGTATACCTAAGGCTGAAAAAAGCCGGCGCGAACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGG


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 62

GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaag ... tgtttaatagCTATTGTTGGTGACATTACCCCATCGGATGGTATACCTAAGGCTGAAAAAAGCCGGCGCGAACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGG


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 104

GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGgtaggtcaag ... tgtttaatagCTATTGTTGGTGACATTACCCCATCGGATGGTATACCTAAGGCTGAAAAAAGCCGGCGCGAACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGG