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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgccgaggggcagtccgcagcaccggttttctgattggttagcaagcaatctgattagctgatacatttgggttggatgctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG

Basic information

species Zea mays
transcript GRMZM2G004352_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 1
--gtgagcgccgaggggcagtccgcagcaccggttttctgattggttagcaagcaatctgattagctgatac-atttgggttggatgctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG
  |     |||      || | |  ||  | |    | |       |       || |   |  ||| | || ||| ||  | |  | |   ||||||   |||||| || || | ||||||| ||||||||||||  |||  ||| ||||||||||||||| |||||||||| || ||||||||||| |||
gtgcatatgcctcctcccatttctgagatctgaacatgtagacaagtgcttgcaaagcgtgtgcgctaagaccattgggacttggggattgagcagAAGGACAGCGAGGAAGTGAAGCAGGCGATGGACCAGCTGAAGGAGCTCGGGTGGGCCAAGCGGTGGAGCTCGCAGCCGTACGTGTCGCGCCGCACG
















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|211057845|gb|FL422564.1|FL422564
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|50329898|gb|CO525024.1|CO525024
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|211212631|gb|FL412327.1|FL412327
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|148930743|gb|EC873038.2|EC873038
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|148954649|gb|EC900096.2|EC900096
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|149084909|gb|EE174419.2|EE174419
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|211463633|gb|FL380567.1|FL380567
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|211057978|gb|FL426568.1|FL426568
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|211087785|gb|FL400777.1|FL400777
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|71313543|gb|DR793346.1|DR793346
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|211403691|gb|FL424169.1|FL424169
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|211110152|gb|FL388603.1|FL388603
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|211493014|gb|FL369799.1|FL369799
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|37417290|gb|CF646298.1|CF646298
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|211472091|gb|FL427745.1|FL427745
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
EST: gi|91872113|gb|EB402070.1|EB402070
EST:     CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAG                         AAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA
genomic: CGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGA

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: 32 (upstream exon), 21 (downstream exon)
Score: 12

CAGCTACGTCGGGCCGCGCCGCCGGTGGCGCGCCGCGGCAGCCTCGTCTTCGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

CAGCTACGTCGGGCCGCGCCGCCGGTGGCGCGCCGCGGCAGCCTCGTCTTCGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG


Block sizes: 29 (upstream exon), 21 (downstream exon)
Score: 1

CAGCTACGTCGGGCCGCGCCGCCGGTGGCGCGCCGCGGCAGCCTCGTCTTCGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 31

CAGCTACGTCGGGCCGCGCCGCCGGTGGCGCGCCGCGGCAGCCTCGTCTTCGGCGGCGTCCGGGGTGGACCTCAAAGCGCTGCAGGCCGCCATCGATAAGgtgagcgccg ... gctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggttagcaagcaatctgattagctgatacatttgggttggatgctgctgcagAAAAGCAGCGATGATGTTAGGCAGGCGCTGGACCAGCTGAGAGAGAGCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG
                            atacattt  TA-rich tract