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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccag

Basic information

species Zea mays
transcript GRMZM2G026470_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 5'ss of exon 5
ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccag
|| || ||||||||||| || || ||||||||||| | |||  |  |||||||||| || ||||| ||||| ||||| ||||| |||||||| |||||||||||||   ||||  |||    ||||        |||| | |  |    ||| ||| |      |  ||||| |   ||    | |     ||| | |  |   | |                                  
ATAGCTGTCTGCGCCGATGATCCTGAGTACCGCCATTTCAATAATCTCAGCGAGCTTTCTCCTCATCGCCTTCAGGAAATCCGGCGCTTCTTTGAAGACTgtacgc--ctgcttcctcagctcatacg----attgctacattttttatgcttggtatt-----gcaccttgatt--tcaattgttttattcttgatcaaaatctttcag-------------------------------
















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|32831350|gb|CD971028.1|CD971028
EST:     TGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
EST: gi|33098670|gb|CF058630.1|CF058630
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
EST: gi|78023075|gb|DV491462.1|DV491462
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTGGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAATGACTTCTTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|28984521|gb|BQ539133.2|BQ539133
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|71331880|gb|DR802818.1|DR802818
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|62550248|gb|DN830668.1|DN830668
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|78121801|gb|DV540185.1|DV540185
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|5499294|gb|AI855161.1|AI855161
EST:     CGAGCTCTCCCCTCNCCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|60354156|gb|DN221129.1|DN221129
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA