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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTTGATCACTACGATGCCCATCTGGTGATATTTGAAAAACTTCCTGATGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctgaatctgagatagactgtagaactgcattgttatctgtattatgctaatctttttggttgaaaaaatcttgcag

Basic information

species Zea mays
transcript GRMZM2G167728_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167728_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g40500.3 (Oryza sativa), 5'ss of exon 2
TTCCTTGATCACTACGATGCCCATCTGGTGATATTTGAAAAACTTCCTGATGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctgaat-------ctgagatagactgtagaactgcattgttatctgtattatgctaatctttttggttgaaaaaatcttgcag
||||||||| |||| |||||| |||||||| || | ||||| || ||  |||| |||||||| ||||||||||||||||| |||||||||||||| ||||||||  ||| | |        |||| |||||  || ||||||| | || |     ||     ||  || ||   |      ||  |||||
TTCCTTGATAACTATGATGCCAATCTGGTGGTAATAGAAAATCTCCCGAATGGTGTGTTTGCTGACCCATTTGAGCTACAACATTTTGTTGAGCGGAAAGgtgatttctaactaagaaaattgaggtagaccatacaactgcaatattcttctctttgcatcaagtttgttttct------atgctgcag
















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|76908362|gb|DV162902.1|DV162902
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|78123012|gb|DV541396.1|DV541396
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|76293670|gb|DV033238.1|DV033238
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|76288285|gb|DV027853.1|DV027853
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|76017739|gb|DT944909.1|DT944909
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|50332870|gb|CO527996.1|CO527996
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCACCCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|40334613|gb|CK368683.1|CK368683
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|78081365|gb|DV509777.1|DV509777
EST:     GGAGTGTTTGCCGACCCCATTTGAGCTACAGCATTTTGTTGAGGGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACTTTGACCTGCCCACAG
genomic: GGAGTGTTTGCCGA-CCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|16925257|gb|BM078325.1|BM078325
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|71416955|gb|DR803872.1|DR803872
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|32827894|gb|CD967572.1|CD967572
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|148944391|gb|EC889498.2|EC889498
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
EST: gi|71432217|gb|DR813267.1|DR813267
EST:     TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAG                         TTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG
genomic: TGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctg ... aatcttgcagTTTTCGTTGATGTTGCTGTTTTTGGAGACGCCAACCTTGAACTGCCCACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTTGATCACTACGATGCCCATCTGGTGATATTTGAAAAACTTCCTGATGGAGTGTTTGCCGACCCATTTGAGCTACAGCATTTTGTTGAGCGCAAAGgtgaaatctgaatctgagatagactgtagaactgcattgttatctgtattatgctaatctttttggttgaaaaaatcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG