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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGATCATAGAGACTGGCGATCCCGTAGCGTTCAAAGAATACCTGCAGGAGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaatgactttctgcttgtcaaaaacctactctcgatgaatgccttccgttttacttcagccactgcattttttttgtttgcttcag

Basic information

species Zea mays
transcript GRMZM2G016827_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016827_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g20270.1 (Oryza sativa), 5'ss of exon 8
GGAGATCATAGAGACTGGCGATCCCGTAGCGTTCAAAGAATACCTGCAGGAGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaatgactttctgcttgtcaaaaacctactctcgatgaatgccttccgtttta-cttcagccactgcattttttttgtttgcttcag
|||||| |||||||||||  |||| |  || |||||  | |||||||| ||||| ||||| |||||||| |||||||||||||||||||| |||||   ||||||         || ||    || ||    |  ||||  |  ||  || |   | || ||||| |  ||  || |  | |  | | | |||
GGAGATAATAGAGACTGGTAATCCAGATGCATTCAAGCAGTACCTGCAAGAGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcg-------ttgtgacgatctaactagtgttctctcttcatttctacttctataacttcatcatctttatgtaatataat-gttccag
















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|211369720|gb|FL088512.1|FL088512
EST:     ACGCCACCCCATCAGCGTCTTCCTTSAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: ACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|5525296|gb|AI861135.1|AI861135
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|32846551|gb|CD986232.1|CD986232
EST:     TACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: TACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|32919020|gb|CF023832.1|CF023832
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|60340840|gb|DN207813.1|DN207813
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|44901134|gb|CK827679.1|CK827679
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|71444030|gb|DR825080.1|DR825080
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|32923072|gb|CF027884.1|CF027884
EST:     ACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: ACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|19272529|gb|BM888785.1|BM888785
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|113701376|gb|EE678880.1|EE678880
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|32805209|gb|CD957445.1|CD957445
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTA
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTA
EST: gi|78107484|gb|DV525902.1|DV525902
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|113704253|gb|EE681757.1|EE681757
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|86474717|gb|DY241087.1|DY241087
EST:     AGTACGAAAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAAATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|32827706|gb|CD967384.1|CD967384
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTA
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTA
EST: gi|12971452|gb|BG267489.1|BG267489
EST:     AGTACGAGAACCCCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|5936778|gb|AW060046.1|AW060046
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|32805446|gb|CD957680.1|CD957680
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTA
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTA
EST: gi|18175413|gb|BM350749.1|BM350749
EST:     AGTACAAGAACGCCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|6012509|gb|AW061946.1|AW061946
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|86474716|gb|DY241086.1|DY241086
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTTTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGTTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
EST: gi|148973068|gb|EE024130.2|EE024130
EST:     AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCAC                         ATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG
genomic: AGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAG

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: 118

GGAGATCATAGAGACTGGCGATCCCGTAGCGTTCAAAGAATACCTGCAGGAGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAGCAGTCCAGCCAGTGCAAGAACATGAGGGATAGCAGCGTGAGCTATGCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 267

GGAGATCATAGAGACTGGCGATCCCGTAGCGTTCAAAGAATACCTGCAGGAGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAGCAGTCCAGCCAGTGCAAGAACATGAGGGATAGCAGCGTGAGCTATGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 209

GGAGATCATAGAGACTGGCGATCCCGTAGCGTTCAAAGAATACCTGCAGGAGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAGCAGTCCAGCCAGTGCAAGAACATGAGGGATAGCAGCGTGAGCTATGCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 288

GGAGATCATAGAGACTGGCGATCCCGTAGCGTTCAAAGAATACCTGCAGGAGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaat ... tttgcttcagATGTTGAAACATTGCTCGACAAAAATTAAGATAGGCTTTGTCCGCTACGAGCAGTCCAGCCAGTGCAAGAACATGAGGGATAGCAGCGTGAGCTATGCAT