Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGCAGAGGAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagcgttgaagcataccctacaaatttcacctgacaaaccttagctaacgcccattacatcttctattaaattcggacag

Basic information

species Zea mays
transcript GRMZM2G103101_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103101_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g52650.1 (Oryza sativa), 5'ss of exon 4
CTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGCAGAGGAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtg---------agcgttgaagcataccctacaaat--ttcacctgacaaa--ccttagctaacgccc---attacatcttcta-----ttaaattcggacag
||||||||||||||||||||||||| |  ||||||||||| |||||||||||||| |||||| | ||  | ||||||||||| ||||||  |||||||||||||||           ||   |||    | | | ||||   || ||||||  ||  || | | |  |  |    | |||| || ||       | |||   | |||
CTGAAACCAAGAGGTACATGGACTTTATCAATCCAGGATCACAAGCAGAGGAAGGAACATTCCTTGGTATCGAGGCTGCACTTGCAGGTTCACAGCCAGGgtaagtacaagaattttgctccgaaatgaagcatccaaacaatttacctgagcaagtccatggttgtctgctttaactacaactactgacattctgaatcttggcag
















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|148995803|gb|EE035034.2|EE035034
EST:     GAAGGGACATTCATAGGGTTAGAGGGTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATTCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|149100655|gb|EE186743.2|EE186743
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|78022949|gb|DV491336.1|DV491336
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGCCCACTGTTCAATCC
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCC
EST: gi|211329944|gb|FL040611.1|FL040611
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGCCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|149077487|gb|EE166183.2|EE166183
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGCCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|94472956|gb|EB701914.1|EB701914
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGCCCACTGTTCAATCCACTAGGACTCGCACAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|32850382|gb|CD990063.1|CD990063
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTTGCAGGCCAACAGCCAGG                         CTACCCCGGGGGCCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|13558835|gb|BG550190.1|BG550190
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|149100656|gb|EE186744.2|EE186744
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|16927444|gb|BM080513.1|BM080513
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|211329938|gb|FL040605.1|FL040605
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGGTC-ACTGTTCAATCCACTAGGACTCGCAAAGG
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGG-TCCACTGTTCAATCCACTAGGACTCGCAAAGG
EST: gi|211329939|gb|FL040606.1|FL040606
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAG
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCC-GGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAG
EST: gi|148994267|gb|EE034026.2|EE034026
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGCCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|148995804|gb|EE035035.2|EE035035
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|148967697|gb|EE018962.2|EE018962
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|148987230|gb|EE031063.2|EE031063
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
EST: gi|16919006|gb|BM073997.1|BM073997
EST:     GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGG                         CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA
genomic: GAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGA

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 3 RNA-Seq libraries.


Block sizes: 28 (upstream exon), 22 (downstream exon)
Score: 1

CTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGCAGAGGAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 134

CTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGCAGAGGAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 35

CTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGCAGAGGAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAGCCAGGgtaagtgagc ... attcggacagCTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG