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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttactgtgttattccttagtattttttgacattttatattttaatagtcatttcactgggtttggtcaatgattgtatgatttgttgattggtag

Basic information

species Zea mays
transcript GRMZM2G035417_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035417_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g15360.1 (Oryza sativa), 5'ss of exon 9
TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttactgtgttattccttagtatttt-ttgacattttatattttaatagtcatt------tcactgggtttggtcaatgat------tgtatgatt-tgttgattggtag
|| ||||| || |||   || |||||||||||||| |||||||||||||||||  ||       | || | ||  | || |||   || | | | ||  ||| ||||       || ||  | || |   | ||      ||    ||| ||||||||   ||
TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatataaatcaactcataagcttcttgttgcttttctttttctttgtagacattaaaatgccagtgcatatgctattttatgtgacttgagcaattctgttgattcacag
















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|16921346|gb|BM075107.1|BM075107
EST:     TCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|5739686|gb|AI947481.1|AI947481
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCCCAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|28983432|gb|BQ538616.2|BQ538616
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|61117480|gb|DN558441.1|DN558441
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTTTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|5932681|gb|AW057042.1|AW057042
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTT-AAGAGCTAG
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAG
EST: gi|60354372|gb|DN221345.1|DN221345
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|120480604|gb|EH210908.1|EH210908
EST:     TTTCAAGCACTCCTTCATTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|93283697|gb|EB675961.1|EB675961
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|17929739|gb|BM266651.1|BM266651
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|60353833|gb|DN220806.1|DN220806
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|5714195|gb|AI944180.1|AI944180
EST:     AGTTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: AGTTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|33102654|gb|CF062614.1|CF062614
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCT
EST: gi|33095687|gb|CF055681.1|CF055681
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTTTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|78024018|gb|DV492405.1|DV492405
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|60339492|gb|DN206465.1|DN206465
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|78121957|gb|DV540341.1|DV540341
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|18167512|gb|BM337351.1|BM337351
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|33091803|gb|CF051797.1|CF051797
EST:     TTTCGAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTTTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|24767328|gb|CA402472.1|CA402472
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTTTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|60353847|gb|DN220820.1|DN220820
EST:     AGTTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: AGTTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|61117483|gb|DN558444.1|DN558444
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTTTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|16925169|gb|BM078237.1|BM078237
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|5847201|gb|AW000280.1|AW000280
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|5325104|gb|AI783295.1|AI783295
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|5152838|gb|AI759136.1|AI759136
EST:     GTTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCCCAAATTCTGCGGTTGATT
genomic: GTTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|61117482|gb|DN558443.1|DN558443
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGATAAACAAAACCCACAAATTTTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|60347941|gb|DN214914.1|DN214914
EST:     TTTCAAGCACTCGTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTTTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|211521982|gb|FL195244.1|FL195244
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|211377507|gb|FL195230.1|FL195230
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|18179525|gb|BM380735.1|BM380735
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
EST: gi|211524979|gb|FL195247.1|FL195247
EST:     TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAG                         CCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT
genomic: TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATT

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), 49 (downstream exon)
Score: 779

TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATTCAGGAAAATCAAGCTGAGTTTCTCCGCTTGGTGAATGAATCTCCTGAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 953

TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATTCAGGAAAATCAAGCTGAGTTTCTCCGCTTGGTGAATGAATCTCCTGAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1052

TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATTCAGGAAAATCAAGCTGAGTTTCTCCGCTTGGTGAATGAATCTCCTGAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 780

TTTCAAGCACTCCTTCAGTTAGTCCAGGCTAATCCTCAAATCTTGCAGgtgcttttac ... tgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATTCAGGAAAATCAAGCTGAGTTTCTCCGCTTGGTGAATGAATCTCCTGAGG