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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccgaattgtcctttgggttgatttgttcatatcaccatatcgagttggttccagtatttcccatcaacacatgaccaacatttaattctgaaatggagacatgaagtaattttttctaatgtttgttttccaatag

Basic information

species Zea mays
transcript GRMZM2G337425_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G337425_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g16570.3 (Oryza sativa), 5'ss of exon 6
GCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccgaattgtcctttgggttg-atttgtt------catatcac---catatcgagttggttccagtatttcccatc-aacacatgaccaac-atttaattctgaaatgg--------agacatgaagtaatt--ttttctaatgtttgttttccaatag
|||| |||||||| || ||||||||||||||||||||| |||||||||| |||||||| || ||||||||||| ||| |   | || ||  |||||||||||||    | ||| |||||| || |  |||| ||      |||| ||    |||    |||      | |  || |   ||  | |  | |||||| || |||||| ||| | |          |   || |||| |     | ||||  || |  | | ||||
GCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGTTCAGGCACATCAGGGAAGTGCCTCTTTCCGAAAAAGgtaagat-gtattatccttttggctacattttttagctggcatagcaaacgcatgataagtctacaactgccttccatctctgataagtaaccaaccatataattccgaatttgtctactttgtatgggatgtaactaaccatttaattcttttgattctatag
















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|18166650|gb|BM336489.1|BM336489
EST:     TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAG                         TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
genomic: TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
EST: gi|148928861|gb|EC873779.2|EC873779
EST:     TCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAG                         TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
genomic: TCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
EST: gi|18164717|gb|BM334556.1|BM334556
EST:     TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAG                         TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
genomic: TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
EST: gi|71760470|gb|DR958407.1|DR958407
EST:     TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTTCCCGAAAAAG                         TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
genomic: TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
EST: gi|78083978|gb|DV512371.1|DV512371
EST:     TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAG                         TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
genomic: TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
EST: gi|78085072|gb|DV513465.1|DV513465
EST:     TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAG                         TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
genomic: TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
EST: gi|76288197|gb|DV027765.1|DV027765
EST:     TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAG                         TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
genomic: TTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
EST: gi|86467324|gb|DY233694.1|DY233694
EST:     CAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAG                         TGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG
genomic: CAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG

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: 48 (upstream exon), 47 (downstream exon)
Score: 57

GCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 23

GCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 35

GCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 32

GCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccga ... tttccaatagTGATGGGCCATCTCAGCTATCGGTTTCTTCAACTGGGTCCGGCAATGAG