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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCCAGCAACTGTGAACCTGCTGGAGATTGAGGATGAAGAGACCGACGGCTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtccctatgatgctacctcagtgcattttttgttatgtcagttagttcactttattttgattcagaaatgcttctgcctggtgttaatcttctt...

Basic information

species Zea mays
transcript GRMZM2G044569_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044569_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g29590.1 (Oryza sativa), 5'ss of exon 2
CAGCCAGCAACTGTGAACCTGCTGGAGATTGAGGATGAAGAGACCGACGGCTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtccc-tatgatgctacctcagtgcattttttgttatgt-cagttagttcactttattttgat--tcagaaatgcttctgcctggtgttaatcttctt
 ||||||||||  ||| |  |||||||||||||||||| ||||||||||| |||||||| | ||||||||||||||| || |||| ||| |||||| |||||||   |||  | |         |   |  |||  || || ||| ||||||| |  |||| |||| ||  |  | ||||||| |  |||  |  ||| |    
AAGCCAGCAACCTTGAGCGCGCTGGAGATTGAGGATGAGGAGACCGACGGTTCTTCTGCAGGGTGCTGCCGCATTTGTCTCGAGACTGATTCTGAGTTAGgtgagtatcctatgtatcagagagtagttttattaatttttctgtgcagttaggttgctttgttttaatatttgggaatgctttt-tctgtgggaaatatg---
















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|47962587|gb|CN845296.1|CN845296
EST:     CTCTTCTGCTGCGTGTTGCCGCATTTGCCTTGAGGCTGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|78085525|gb|DV513918.1|DV513918
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|71766873|gb|DR964810.1|DR964810
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|71764260|gb|DR962197.1|DR962197
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|89253176|gb|DY624962.1|DY624962
EST:     ATCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|71449470|gb|DR830520.1|DR830520
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCGGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|78075719|gb|DV504153.1|DV504153
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|78085425|gb|DV513818.1|DV513818
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|74242907|gb|DT650821.1|DT650821
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|91875640|gb|EB405597.1|EB405597
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|149051784|gb|EE155909.2|EE155909
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|76287272|gb|DV026840.1|DV026840
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|91877670|gb|EB407627.1|EB407627
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|26457371|gb|CA828954.1|CA828954
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|67025393|gb|CO454142.1|CO454142
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
EST: gi|211122360|gb|FL034211.1|FL034211
EST:     CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAG                         GTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC
genomic: CTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtcc ... gtttttgcagGTGATGAGCTAATATCACCTTGCATGTGCAAGGGAACTCAGCAGTTTGTTC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCCAGCAACTGTGAACCTGCTGGAGATTGAGGATGAAGAGACCGACGGCTCTTCTGCTGCGTGCTGCCGCATTTGCCTTGAGAATGAGTCTGAGATAGgtgatggtccctatgatgctacctcagtgcattttttgttatgtcagttagttcactttattttgattcagaaatgcttctgcctggtgttaatcttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC