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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatacgatatagattctctccattggtatcacctctgtccatggttataaagttgctctcgtctttggcagATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGTTGGAGACTATGGTTGGTTTCAGTTGCTATCGGCCTTGTGAG

Basic information

species Zea mays
transcript GRMZM2G132712_T01
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 32
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 16
gtaacatacgatatagattctctcc--attg--gtatcacctctgtc-catggtt-----ataaagttgctctcgtctttggcagATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGTTGGAGACTATGGTTGGTTTCAGTTGCTATCGGCCTTGTGAG
||||||   ||||  | |  |   |  | ||   ||||| |  |  | ||||  |     ||||||||||| || | || |||||||||| || ||| |||||||||| |||||||||||||  ||||| |||  ||||||| |||||||||| ||||||||||| ||| || | ||
gtaacaactgatagtgttctttcgctgaatgccctatcatccttaccacatgaattgctgataaagttgctgtcctgttcggcagATACTAATTATTGAGTTCCTGGGAAAGTTCTTCAAAACTGTGAGACTTAATTGGAGATTATGGTTGGTCTCAGTTGCTATTGGCATTATAAG
















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|5846745|gb|AI999828.1|AI999828
EST:     CGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAGTATTTCAG                         ATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGT
genomic: CGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAGTATTTCAGgtaacatacg ... tctttggcagATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGT
EST: gi|5296205|gb|AI782885.1|AI782885
EST:     CGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAGTATTTCAG                         ATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGT
genomic: CGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAGTATTTCAGgtaacatacg ... tctttggcagATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGT
EST: gi|6020890|gb|AW065818.1|AW065818
EST:     CGAAGAATCACCTGTTCATGGGAATAATCGTTATAACGACAGTATTTCAG                         ATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGN
genomic: CGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAGTATTTCAGgtaacatacg ... tctttggcagATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGT
EST: gi|60340338|gb|DN207311.1|DN207311
EST:     CGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAGTATTTCAG                         ATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGT
genomic: CGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAGTATTTCAGgtaacatacg ... tctttggcagATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccattggtatcacctctgtccatggttataaagttgctctcgtctttggcagATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGTTGGAGACTATGGTTGGTTTCAGTTGCTATCGGCCTTGTGAG
                                    ttgctctcgtcttt  CT-rich tract
                            ttataaagtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatacgatatagattctctccattggtatcacctctgtccatggttataaagttgctctcgtctttggcagATACTGATAATTCAGTTCCTGGGGAAGTTCTTCAAAATAGTGAGGCTTGGTTGGAGACTATGGTTGGTTTCAGTTGCTATCGGCCTTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA