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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGTCGTCGCAGGAGGACCCGCGATGTCGCACTTCGGGAGGTCAGGCCCGCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggagatctaaccctagcccctccagccccacccaccctccctactctctctctccctctctccctaatcgcttccttctcgtatccgtctcccccccgcttcacag

Basic information

species Zea mays
transcript GRMZM2G016296_T06
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016296_T06 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 5'ss of exon 1
GCCGTCGTCGCAGGAGGACCCGCGATGTCGCACTTCGGGAGGTCAGGCCCGCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggagatctaaccctagcccctccagccccacccaccctccctactctctctctccctctctccctaatcgcttccttctcgtatccgtctcccccccgcttcacag
| || ||     ||    | ||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||  |   ||| |||||||       || || | | |        ||| ||| | ||  ||    |||||||         ||| |||| | ||  ||  | || |||
GGCGGCGGGCGGGGGTTTCTCGCCATGTCGCACTTCGGGAGGTCGGGGCCGCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagcaaaccctagccctagcgggaatcgctccgctcgcta-----gctcgctcgccccacctt---ctaatcgg--------cgtttccgccgccttcct-cctcgcag
















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|87157632|gb|DY402421.1|DY402421
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|18384287|gb|BM417486.1|BM417486
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|9731359|gb|BE510111.1|BE510111
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTAC
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTAC
EST: gi|71766439|gb|DR964376.1|DR964376
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|74235570|gb|DT643484.1|DT643484
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|71421374|gb|DR805394.1|DR805394
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|211456040|gb|FL150302.1|FL150302
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|6022225|gb|AW067153.1|AW067153
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|37417209|gb|CF646257.1|CF646257
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|76280364|gb|DV019932.1|DV019932
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|22489702|gb|BU049625.1|BU049625
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|211456031|gb|FL150293.1|FL150293
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|26558961|gb|CA831196.1|CA831196
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|76936777|gb|DV174882.1|DV174882
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|50336916|gb|CO532042.1|CO532042
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|22545919|gb|BU098278.1|BU098278
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|74232258|gb|DT640172.1|DT640172
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|211456033|gb|FL150295.1|FL150295
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGA-SSCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|211456029|gb|FL150291.1|FL150291
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|211456036|gb|FL150298.1|FL150298
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|91873269|gb|EB403226.1|EB403226
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
EST: gi|211456038|gb|FL150300.1|FL150300
EST:     GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCC                         GCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggaga ... cgcttcacagGCACCACGGCCGACGACCTCTTCCCGCTCTTCGAGCGCTACGGCAAGGTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGTCGTCGCAGGAGGACCCGCGATGTCGCACTTCGGGAGGTCAGGCCCGCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagggagatctaaccctagcccctccagccccacccaccctccctactctctctctccctctctccctaatcgcttccttctcgtatccgtctcccccccgcttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT