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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgctatatgtgaatcagtgctttctctgtctaacaccaattgggcatagtttaattttttttccttgttttacag

Basic information

species Zea mays
transcript GRMZM5G862538_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862538_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g01240.1 (Oryza sativa), 5'ss of exon 37
TGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgta-catgctatatgtgaatcagtgctttctctgt----ctaacaccaattgggcatagtttaattttttttccttgttttacag---------------
|||  |||||||||| ||||||||||||||||||||||||||||||  ||||  |||||   |||||||| ||  ||| ||  ||| ||||||| | |||||| |    | | | |  |  | |  |||||   |    |||||   | || |  ||  ||   |||   |    |  |||   |               
TGACATGATTCCTTCCAGTTGCATTCAAATGCGCAATGTCATTCTTGATGCTCATCCACAAGACATGAGAGTGGTAGATCCAGCTAGTCCTAATTTGAAGgtagccatttgtttttacaataatattttcttcattctcctaactttagttagagatttttgtttttgactgaaatacttttagggctttgcctgacagt

upper sequence: GRMZM5G862538_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S85_31V6.1 (Physcomitrella patens), 5'ss of exon 46
TGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgta-catgct-atatgtg-aatcagtgctttctctgtctaac--accaattgggcatagttt--aattttttttccttgttttacag------------------------------------------------------------
||||||||||||  ||   || ||||| ||||||||| | |||||||| ||||||||||| |||||| |||| || || |||| ||| |||||| | |||||| |||  | |||| |  || |       | |     || |  | |||||  |   | |||  ||   |   |  ||  |||   |                                                            
TGATGTGATTCCCCCATCCTGTATTCAGATGCGCAATCTAATTCTTAGCGCTTTTCCACGCAACATGCGACTTCCTGATCCTTTTACACCTAATTTGAAGgtagcatattcatattttcaaccttcaaactttgcagatagcctatcaattttgttcatttttaaaaagtaaatatttcctttgtggctgttatatgtaaattggaaggcacaaaagtcagctatctaaggcgtggtgtttaatcag
















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|22491140|gb|BU051063.1|BU051063
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
EST: gi|19272457|gb|BM888713.1|BM888713
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
EST: gi|33285664|gb|CF075459.1|CF075459
EST:     NTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
EST: gi|38229577|gb|CF919890.1|CF919890
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAG                         ATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
EST: gi|67027758|gb|CO456507.1|CO456507
EST:     CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAG                         ATTGATTTATTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT
genomic: CTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTT

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), 49 (downstream exon)
Score: 55

TGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTTGATGGTACCCTCAAATCAAAGCAGTTGAAGACTGAGTTTGATGAATATC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 44

TGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTTGATGGTACCCTCAAATCAAAGCAGTTGAAGACTGAGTTTGATGAATATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

TGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTTGATGGTACCCTCAAATCAAAGCAGTTGAAGACTGAGTTTGATGAATATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

TGATGTGATTCCTTCAAGTTGCATTCAAATGCGCAATGTCATTCTTAGTGCTTTTCCACGTAACATGAGACTGCCAGACCCTTCTACTCCTAATCTAAAGgtacatgcta ... tgttttacagATTGATTTGTTGGCTGAAATTTCAATAGCACCACGAATCATGTCAGATGTTGATGGTACCCTCAAATCAAAGCAGTTGAAGACTGAGTTTGATGAATATC