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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagttccttcatgttttacttcactgatttctcttgttcccaattcttacagatatcctgtttactag

Basic information

species Zea mays
transcript GRMZM2G412888_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412888_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g41730.2 (Oryza sativa), 5'ss of exon 4
GTATGGTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagttccttcat---gttttacttcactgatttctcttgttcccaattc--ttacagatatcctgtttactag
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GTATGGTGAGAGTGATGGTTATCCTTCTCAGAAGGGCATCATAAATGATGCACAGgtttgctgattcgttcaatcggttttatgttaa-gttttctgtttctgtctattctcttactgctctctt-tttaatag
















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|26557244|gb|CA829479.1|CA829479
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|71425140|gb|DR806559.1|DR806559
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|76018058|gb|DT945228.1|DT945228
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|71430933|gb|DR811983.1|DR811983
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|71427907|gb|DR808957.1|DR808957
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|89250823|gb|DY622609.1|DY622609
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|29129758|gb|CB380462.1|CB380462
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|149008856|gb|EE041069.2|EE041069
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|71448310|gb|DR829360.1|DR829360
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|89253014|gb|DY624800.1|DY624800
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|148933213|gb|EC876864.2|EC876864
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|148939301|gb|EC883808.2|EC883808
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|31664225|gb|CD572950.1|CD572950
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|30705302|gb|CD058738.1|CD058738
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|76293689|gb|DV033257.1|DV033257
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|89252853|gb|DY624639.1|DY624639
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|211038058|gb|FL324597.1|FL324597
EST:     CATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: CATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|67011215|gb|CO439964.1|CO439964
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACCAACCAG-AT
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACAC-AACCAGGAT
EST: gi|8103365|gb|AW928006.1|AW928006
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|91055111|gb|EB165529.1|EB165529
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|67041292|gb|CO467547.1|CO467547
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|29576736|gb|CB616848.1|CB616848
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|148947394|gb|EC892802.2|EC892802
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|149014757|gb|EE044444.2|EE044444
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|71437275|gb|DR818325.1|DR818325
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
EST: gi|148933571|gb|EC877438.2|EC877438
EST:     GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAG                         GCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA
genomic: GTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATA

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: 209

GTATGGTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

GTATGGTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

GTATGGTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

GTATGGTGAGAGTGATGGTTATCCTTCTCAGAAAGGGATCACATATGATGCACAGgtctgttagt ... tgtttactagGCTGCACTTGACCATCTAGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCA