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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaatgactttgtttccatcctcgatgtctatttcatggtctgttcatgacactgaatgctcattttggcttatgcttgtagatgttcctagtgt...

Basic information

species Zea mays
transcript GRMZM2G061419_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061419_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 5'ss of exon 5
GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaatgactttgtttccatcctcgatgtctatttcatggtctgttcatgacactgaatgctcattttggcttatgcttgtagatgttccta-gtgt
|||||  |||||||||||||||| || |||||| | |||||||| |||||||||||||| || ||||| || ||  |||||| ||||  ||  |  ||| ||||| |  | | |  ||  |     |  ||| | ||| || | ||    |      | |||| | |   |||
GACAAGTTGGAGGCAAAGGTGGTTGTAGCTGGGCTCTCAACAACATGTAGCCAGAAAATCCATAATCAGTTAgtacgtaaatcacttcattctcgcccttgatgtgttatcctttttcactatgcaaagctgga-gcttatctaggtcattctaaacacatgtacttgcatgt

upper sequence: GRMZM2G061419_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G35860.1 (Glycine max), 5'ss of exon 4
GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaatgactttgtttccatcctcgatgtctatttcatggtctgttcatgacactgaatgctcattttggcttatgcttgtagatgt-tcctagtgt-
||  || | || || ||||| || ||  |||| ||||||||||| ||||| || |||||||||||||||||||| ||  | |   ||    |  ||  | |||   | ||| |    |      |  |  ||    |    | |       ||||    || | | |   | | 
GATCATGTTGAAGCTAAGGTTGTTGTATCTGGTTTGTCAACAACTTGTAGTCAAAAAATTCACAATCAATTGgtatgggattttgttgacatatatt-ttgatagtttttttaactacaaaatgtagccttgggc-catgctatattcagagcttaaccatatcttcctttata

upper sequence: GRMZM2G061419_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G01130.1 (Glycine max), 5'ss of exon 4
GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaatgactttgtttccatcctcgatgtct---atttcatggtctgttcatg--acactgaatgctcattttggcttatgcttgtagatgttcctagtgt
||   | |  | || | | |  |  | ||||| || |||||||| ||||| || |||||||||||||||||||| ||    |    || |      ||    | | |   | | ||  ||  |  |||   | | |  |  |  |||||   |||||    | | || | |      
GATTCTGTTAAAGCTAGGATTATAATAGCTGGTTTATCAACAACTTGTAGTCAAAAAATTCACAATCAATTGgtatgattttattcttatactttgccctagtattttcaaatgcaaagtagggccatactatatttgaaacatattttca-ttatgacacttgctgattcat----

upper sequence: GRMZM2G061419_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G03760.1 (Glycine max), 5'ss of exon 5
GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaatgactttgtttccatcctcgatgtctatttcatggtctgttcatgacactgaatgctcattttgg--cttatgcttgtagatgttcctagtgt--
||  || | || || ||||| || || ||||| ||||||||||| ||||| || |||||||||||||||||||| |   | |   ||    |  ||  |||||   | |||||   | |   | ||   |   |||||   ||  |  ||||  |||||     ||  || | |  
GATCATGTTGAAGCTAAGGTTGTTGTAGCTGGTTTGTCAACAACTTGTAGTCAAAAAATTCACAATCAATTGgtataggattttgttgacatatatt-tcgatagttttttcaaaatgtagccttgggcc---atgctatattcagaacttaaccttgtcttcctttatatttttt

upper sequence: GRMZM2G061419_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 5'ss of exon 5
GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaatgactttgtttccatcctcgatgtctatttcatggtctgttcatgaca---ctgaatgctcattttggcttatgcttgtagatgttcctagtgt---------------------------------------------------------------------------------
||  || | || || ||||| || |||||||| || |||||||| ||||||||||||||||| ||||| ||||| |||  |||| ||| |||   ||| | || | | ||| ||      ||  ||||    || ||  |   | |   |  |  | || | |  |  ||  | |                                                                                 
GATCATGTTGAAGCTAAGGTCGTGGTTGCTGGTTTATCAACAACATGTAGCCAGAAAATTCATAATCAGTTGgtatgt--atgattttttttttctcc-caatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaag

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|71427423|gb|DR808473.1|DR808473
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|149075471|gb|EE163995.2|EE163995
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|76913089|gb|DV165003.1|DV165003
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|74245609|gb|DT653523.1|DT653523
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|61119317|gb|DN560278.1|DN560278
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|78090711|gb|DV519085.1|DV519085
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|148972415|gb|EE023349.2|EE023349
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|71304141|gb|DR788190.1|DR788190
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|71447226|gb|DR828276.1|DR828276
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|71427209|gb|DR808259.1|DR808259
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|76020824|gb|DT947994.1|DT947994
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|149076827|gb|EE165480.2|EE165480
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|148965663|gb|EE016513.2|EE016513
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGNAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|148969660|gb|EE020524.2|EE020524
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
EST: gi|76293199|gb|DV032767.1|DV032767
EST:     TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTG                         ATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT
genomic: TCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGAT

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), 49 (downstream exon)
Score: 277

GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 136

GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

GACAATCTGGAGGCAAAGGTGGTCGTTGCTGGGTTGTCAACAACCTGTAGCCAGAAAATTCACAATCAATTGgtttgtaaat ... actgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA