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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtttcgcctgcctttgttctgatcgagtctaattgttgctaatgataccgactcactggccaacgtctgttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCCGGGGGCCACGCTGAGCTTTATCGTTCCCCTGCTGTCGGCTCCCTTGCAA

Basic information

species Zea mays
transcript GRMZM2G027571_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027571_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 3'ss of exon 3
----gtttggtttcgcctgcctttgttctgatcgagtctaattgttgctaatgataccgactcactggccaacgtctgttc-tgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCCGGGGGCCACGCTGAGCTTTATCGTTCCCCTGCTGTCGGCTCCCTTGCAA---
    |      ||| ||| ||  | |  |  | |||| | || | | | |    || | | | ||   ||||  |  |||  |   |||| || |||||||||||||| ||||| || |||||||| |||||||||||||||||||   |||||||||| |  |||||    |   |   | ||||||    
gtatgaaaaagttcccctacccatctagtt-ttgagtttgatcgatacaagaactatcaattgacctaccaatcttcgtttgtaaccagGGAAACCTTTGGGGCGTGGGCGCGGACGCGGTCGTGGCCGTGGTCGGGGCCGGGGGC---GCTGAGCTTTGTTATTCCCTGTTTTGTGAAGCTCTTGCAGTGC
















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|91057155|gb|EB167573.1|EB167573
EST:     CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAG                         GAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
genomic: CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAGgtttggtttc ... ttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
EST: gi|76293638|gb|DV033206.1|DV033206
EST:     CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAG                         GAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
genomic: CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAGgtttggtttc ... ttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
EST: gi|29945138|gb|CB815488.1|CB815488
EST:     CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAG                         GAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
genomic: CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAGgtttggtttc ... ttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
EST: gi|45847704|gb|CN071647.1|CN071647
EST:     CCTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAG                         GAAAGCCCTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
genomic: CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAGgtttggtttc ... ttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
EST: gi|71445025|gb|DR826075.1|DR826075
EST:     CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAG                         GAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
genomic: CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAGgtttggtttc ... ttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
EST: gi|88749844|gb|DY533985.1|DY533985
EST:     CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAG                         GAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC
genomic: CTTGCTGGTAGAGGAAACCCCTAGGGTGAAGCCTAAGAAGCCAACTACAGgtttggtttc ... ttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtctaattgttgctaatgataccgactcactggccaacgtctgttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCCGGGGGCCACGCTGAGCTTTATCGTTCCCCTGCTGTCGGCTCCCTTGCAA
                         gactcac  putative branch site (score: 2)
                                         tctgttct  putative PPT
     taattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggtttcgcctgcctttgttctgatcgagtctaattgttgctaatgataccgactcactggccaacgtctgttctgtgcagGAAAGCCTTTGGGGCGTGGTCGCGGCCGAGGTCGTGGACGTGGTCGGGGCCGGGGGCCACGCTGAGCTTTATCGTTCCCCTGCTGTCGGCTCCCTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT