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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAAGAGCAACTTCAAGTTGCTATCAGATGAAGAGTTTGATATTGCGCAATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttttttttacagaaaaattaaaatagacttagtaacttacatgactagtattttgttgacgatctatttgctaaccttgaaatgcag

Basic information

species Zea mays
transcript GRMZM2G011136_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011136_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 5'ss of exon 4
GGAAAAGAGCAACTTCAAGTTGCTATCAGATGAAGAGTTTGATATTGCGCAATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttttttttacagaaaaattaaaatagacttagtaac-ttacatgactagtattttgttgacgatctatttgctaaccttgaaatgcag
|||||||||||||||||||||| |||| |||||||||| |||| |||| ||||||||||||||| | | || ||||| || ||||||||||| ||||||| || | | | || || | ||||| || |||| || | || || | ||| | | ||||| || ||
GGAAAAGAGCAACTTCAAGTTGTTATCTGATGAAGAGTATGATGTTGCACAATCTGGAAAATATCTTCTAAACCTTCCCATAAAAGTTGATGAGCCTAAGgtctggaactat------ggccttttcaagcatgtactgtaacgtttcatg--------ttcg--gatgactgaattgatttcgttgaattgtag

upper sequence: GRMZM2G011136_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT3G19340.1 (Arabidopsis thaliana), 5'ss of exon 4
GGAAAAGAGCAACTTCAAGTTGCTATCAGATGAAGAGTTTGATATTGCGCAATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttttttttacagaaaaattaaaatagacttagtaacttacatgactagtattttgttgacgatctatttgctaaccttgaaatgcag
||| ||||||||||| || | | |||||||| | || |||| || ||||| | ||| | | |||||||| |||||||||||||| ||||||||||| |||| | ||| || | | ||| | | || | ||| | | | ||||| || | || ||
GGAGAAGAGCAACTTTAAAATAACAAGTAATGAAGAGATGGAAGTTGCACACTCTGGGCAGTATCTTCTCAATCTTCCCATCAAAGTTGATGAGTCTAAGgtttg-------tttaaacaaactttcactaatgcttgtgtgttgccgggattcttata----aaatagttttcttgcttttggtgga-tgaag

upper sequence: GRMZM2G011136_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0068g00980.t01 (Vitis vinifera), 5'ss of exon 4
GGAAAAGAGCAACTTCAAGTTGCTATCAGATGAAGAGTTTGATATTGCGCAATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttttttttacagaaaaattaaaatagacttag-taacttacatgactagtattttgttgacg-atctatttgctaaccttgaaatgcag---------------------------------------------------
||| || |||||||||| | | | ||||||| ||| |||| ||||| | ||||| ||||| |||||||||| |||| ||||||||||||||||| |||||| | | | | || || | | | ||| | | | |||||| | | | || || | || | || ||
GGATAAAAGCAACTTCAGGCTAACAACAGATGATGAGGTTGAGATTGCACTTTCTGGGCAATATCGTCTGAATCTTCCTATCATTGTTGATGAATCTAAGgtatgatttatctgaata-aagtatagatacacactgaaattagatacatgcatgtatgcctataaacacattcacttttgtctttagagatttcatttgtgttttacatctgctgatcttagtgttcacttttttcctgaatgtag

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|6020843|gb|AW065771.1|AW065771
EST:     AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
EST: gi|71767791|gb|DR965728.1|DR965728
EST:     AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
EST: gi|211454006|gb|FL153959.1|FL153959
EST:     AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
EST: gi|71445898|gb|DR826948.1|DR826948
EST:     AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
EST: gi|211454007|gb|FL153960.1|FL153960
EST:     AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACGAGAAGTTGTTGACAA
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAA
EST: gi|5325032|gb|AI783223.1|AI783223
EST:     AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
EST: gi|32931583|gb|CF036395.1|CF036395
EST:     AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
EST: gi|13559022|gb|BG550377.1|BG550377
EST:     AATCTGGAAAATATTCGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
EST: gi|5846844|gb|AI999927.1|AI999927
EST:     AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAG                         CTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT
genomic: AATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAAT

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), 49 (downstream exon)
Score: 96

GGAAAAGAGCAACTTCAAGTTGCTATCAGATGAAGAGTTTGATATTGCGCAATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAATCTACCAGAGTTTTCAAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

GGAAAAGAGCAACTTCAAGTTGCTATCAGATGAAGAGTTTGATATTGCGCAATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAATCTACCAGAGTTTTCAAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

GGAAAAGAGCAACTTCAAGTTGCTATCAGATGAAGAGTTTGATATTGCGCAATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAATCTACCAGAGTTTTCAAACAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 211

GGAAAAGAGCAACTTCAAGTTGCTATCAGATGAAGAGTTTGATATTGCGCAATCTGGAAAATATTTGTTGAATCTTCCGATCAAAGTTGATGAATCTAAGgtttgatttt ... tgaaatgcagCTAGACAAGAAGTTGTTGACAAAATATTTTAAAGAGCACCCACATGACAATCTACCAGAGTTTTCAAACAAG