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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATGGTGGTGCTAAGGTAGCAGAGTATGTTAAAGAAAACCTGTTCAACAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactcttgctctttttcccgctaacatcagttgcttatgtgaatgcaaccatgagggcttgagcttgtgtgtttgtattactgcag

Basic information

species Zea mays
transcript GRMZM2G056572_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056572_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 3
GTCATGGTGGTGCTAAGGTAGCAGAGTATGTTAAAGAAAACCTGTTCAACAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactcttgctctttttcccgctaacatcagttgct----tatgtgaatgcaaccatgagggcttgagcttgtgtgtttgtattactgcag
|||||||||||||||| ||||| |||||||||||| | || || ||||   ||||| | || |||||||||||||||||||| || ||||| || ||||||||    ||| ||| |||||      ||  || || |    | |||| ||  ||     ||  ||  | |  |||   |||| || ||| ||
GTCATGGTGGTGCTAAAGTAGCTGAGTATGTTAAACAGAATCTCTTCAGTCATCTTCTAAGGCATCCAAAGTTCATCAGTGACACCAAAGTGGCAATAGgtattggtttgttctctttccataattcactagatgttgagttttgtgtatagaattgacagaact--accacgtgatattgt-ttgctgtag
















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|87156931|gb|DY401720.1|DY401720
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|71762691|gb|DR960628.1|DR960628
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|211062962|gb|FL387714.1|FL387714
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|211113689|gb|FL397728.1|FL397728
EST:     AATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGT
genomic: AATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTC-GCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGT
EST: gi|149111016|gb|EE294515.2|EE294515
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|211036167|gb|FL457683.1|FL457683
EST:     AAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: AAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|76931265|gb|DV172687.1|DV172687
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|5296366|gb|AI783136.1|AI783136
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|60394530|gb|DN227400.1|DN227400
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|67024109|gb|CO452858.1|CO452858
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTTGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|76917080|gb|DV166669.1|DV166669
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|149106821|gb|EE188718.2|EE188718
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|211036166|gb|FL457682.1|FL457682
EST:     AGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTC-TAGAATCTGACAGTAGTC
genomic: AGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|31406344|gb|CD485076.1|CD485076
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|74237808|gb|DT645722.1|DT645722
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|26558429|gb|CA830664.1|CA830664
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|94472146|gb|EB701104.1|EB701104
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|211142820|gb|FL374557.1|FL374557
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|5846990|gb|AW000069.1|AW000069
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|60351289|gb|DN218262.1|DN218262
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|18660188|gb|BM500731.1|BM500731
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|91051774|gb|EB162192.1|EB162192
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|76290021|gb|DV029589.1|DV029589
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|76288715|gb|DV028283.1|DV028283
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|22133680|gb|BQ833845.1|BQ833845
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|37425087|gb|CF650279.1|CF650279
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|211187859|gb|FL425729.1|FL425729
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|50323711|gb|CO518837.1|CO518837
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|211209068|gb|FL368391.1|FL368391
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|60359261|gb|DN226234.1|DN226234
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|71448387|gb|DR829437.1|DR829437
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|67021956|gb|CO450705.1|CO450705
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTTGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
EST: gi|101386844|gb|EB815439.1|EB815439
EST:     CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAG                         ATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC
genomic: CAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTC

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: 248

GTCATGGTGGTGCTAAGGTAGCAGAGTATGTTAAAGAAAACCTGTTCAACAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTCAAAATCAATGCGGGTCAACTGCATCAACTGCTGTACTTGTTGGTGATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

GTCATGGTGGTGCTAAGGTAGCAGAGTATGTTAAAGAAAACCTGTTCAACAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTCAAAATCAATGCGGGTCAACTGCATCAACTGCTGTACTTGTTGGTGATCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 288

GTCATGGTGGTGCTAAGGTAGCAGAGTATGTTAAAGAAAACCTGTTCAACAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTCAAAATCAATGCGGGTCAACTGCATCAACTGCTGTACTTGTTGGTGATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

GTCATGGTGGTGCTAAGGTAGCAGAGTATGTTAAAGAAAACCTGTTCAACAATCTTGTTAGTCATCCAAAGTTCATCAGTGATACTAAAGTCGCTATAGgtatactctt ... attactgcagATGATGCTTATAAAAGCACCGACAGTGAATTCTTAGAATCTGACAGTAGTCAAAATCAATGCGGGTCAACTGCATCAACTGCTGTACTTGTTGGTGATCG