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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctccctaacctctcatcctcgctaatatctttcaccgaactactttgccctttggtatgtatgatgtgttttgctaacaagtttatcttttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCTGACCATGAGGCTGTCATTGCAAGAATTCAGATCAGCATAAAAAATTGCT

Basic information

species Zea mays
transcript GRMZM2G038667_T02
intron # 9
splice site 3'
intron type U2

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|33096496|gb|CF056490.1|CF056490
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACNNNNNNNTGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT
EST: gi|6973544|gb|AW438280.1|AW438280
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAA-TGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT
EST: gi|148948172|gb|EC893687.2|EC893687
EST:     TGGCCGGACGAAATATGACTTTTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACNNNNNNNTGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT
EST: gi|6021566|gb|AW066494.1|AW066494
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAA-TGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT
EST: gi|78179119|gb|DV549492.1|DV549492
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTTCA-GTATAGTACAAAAAA-TGC
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTT-CAAGTATAGTACAAAAAAATGC
EST: gi|71767671|gb|DR965608.1|DR965608
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACNNNNNNNTGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT
EST: gi|211525354|gb|FL435359.1|FL435359
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACNNNNNNNTGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT
EST: gi|6964721|gb|AW433414.1|AW433414
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCANAGCTGTTGTATGTTCAAGTATAGTACAAAAAA-TGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT
EST: gi|71435798|gb|DR816848.1|DR816848
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACNNNNNNNTGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT
EST: gi|149014737|gb|EE044418.2|EE044418
EST:     TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATG                         TTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACNNNNNNNTGCT
genomic: TGGCCGGACGAAATATGACTTCTGAACTTTTGGGTTAAAACTGACACATGgtatcctccc ... ttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgccctttggtatgtatgatgtgttttgctaacaagtttatcttttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCTGACCATGAGGCTGTCATTGCAAGAATTCAGATCAGCATAAAAAATTGCT
                           tgctaac  putative branch site (score: 1)
                                     tttatcttttccttac  putative PPT
                                     tttatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctccctaacctctcatcctcgctaatatctttcaccgaactactttgccctttggtatgtatgatgtgttttgctaacaagtttatcttttccttacagTTGATACTGTTCAAAGCTGTTGTATGTTCAAGTATAGTACAAAAAAATGCTGACCATGAGGCTGTCATTGCAAGAATTCAGATCAGCATAAAAAATTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA