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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttcttatatagtttctattcaatcacttcctttttccattgtcacccagtaacatatacttgttgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGACATCTATAATGTTCCCTTCAAAGCGTTTGATGAGGTTCTTGATATGGAAA

Basic information

species Zea mays
transcript GRMZM2G461793_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g16950.5 (Oryza sativa), 3'ss of exon 5
gttattttcttatatagtttctattcaatcacttcctttttccattgtcacccagt-aacatatacttgttgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGACATCTATAATGTTCCCTTCAAAGCGTTTGATGAGGTTCTTGATATGGAAA
         |||| || ||   || | |||    || |||     | |  |  | | ||||| ||| |||||  |||||||||||||||| |||||||||||||||  |||| |||||||| |||| ||||||||||||   |||||||||||  |||||     ||||||| |||||||
--------gttat-tatttctgatgctatccacgccctttgatggtttgccttattgaacatgtacctgttgtcatgcagAATATTGAAAGTGAATTGAAGGAACGGTTGAAGAAAGGTGTCTATGGTGACATCTATAACTATCCCTTCAAAGAATTTGACACTATTCTTGAAATGGAAA
















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|93012902|gb|EB638422.1|EB638422
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|71330256|gb|DR801876.1|DR801876
EST:     TGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTNCA-CTAGAAAGG                         AATATTGAAAATGAAT
genomic: TGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCT-CAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAAT
EST: gi|148939429|gb|EC883983.2|EC883983
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCT
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCT
EST: gi|33468206|gb|CF245255.1|CF245255
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|211374387|gb|FK951695.1|FK951695
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|71322070|gb|DR797725.1|DR797725
EST:     GTGATTTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|31355775|gb|CD440132.1|CD440132
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|76932105|gb|DV172945.1|DV172945
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|148946083|gb|EC891379.2|EC891379
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAGAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|211374386|gb|FK951694.1|FK951694
EST:     TGATCTCCAGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGAWGTTTATGCTGA
genomic: TGATCTCC-GGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGG-TGTTTATGCTGA
EST: gi|91872818|gb|EB402775.1|EB402775
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|148953457|gb|EE152960.2|EE152960
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|148987549|gb|EE031414.2|EE031414
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|148987550|gb|EE031415.2|EE031415
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACGAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|94477914|gb|EB706872.1|EB706872
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         GATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|211360103|gb|FL362300.1|FL362300
EST:     TGATCTCCGGAGAATGGAGAAAAGCTGAA-GGGCTGCTCAACTAGAAAGG                         GATATTGAAAATGAATTGGAGGGACGCCTTGA-CAAAG-TGGTTATGCTGA
genomic: TGATCTCCGGAGAATGGAGAAA-GCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCT-GAACAAAGGTGTTTATGCTGA
EST: gi|60395012|gb|DN227881.1|DN227881
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|71322072|gb|DR797726.1|DR797726
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|31355774|gb|CD440131.1|CD440131
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|148953458|gb|EE152961.2|EE152961
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
EST: gi|91872817|gb|EB402774.1|EB402774
EST:     GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGG                         AATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC
genomic: GTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGAC

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

GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGACATCTATAATGTTCCCTTCAAAGCGTTTGATGAGGTTCTTGATATGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGACATCTATAATGTTCCCTTCAAAGCGTTTGATGAGGTTCTTGATATGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGACATCTATAATGTTCCCTTCAAAGCGTTTGATGAGGTTCTTGATATGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

GGAGAAGGTCATGACAATGCCCAGGAAGCAAACACAGCGTGATCTCCGGAGAATGGAGAAAGCTGAAAGGGCTGCTCAACTAGAAAGGgttattttct ... tgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGACATCTATAATGTTCCCTTCAAAGCGTTTGATGAGGTTCTTGATATGGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatcacttcctttttccattgtcacccagtaacatatacttgttgctatgcagAATATTGAAAATGAATTGAAGGAACGCCTGAACAAAGGTGTTTATGCTGACATCTATAATGTTCCCTTCAAAGCGTTTGATGAGGTTCTTGATATGGAAA
                            cagtaac  putative branch site (score: 151)
                               taacatata  TA-rich tract