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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtatttgtctctaattcgtcccttgttaatgaatattgctcaaaatctctgtatgtgataaaaaactgagggatgtaactggcgtttgttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAG

Basic information

species Zea mays
transcript GRMZM2G062425_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062425_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g21830.1 (Oryza sativa), 3'ss of exon 1
tttgtatttgtctctaattcgtcccttgttaatg-aatattgctcaaaatctctgtatgtga-taaaaaactgagggatgtaactggcgtttgt-tttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAG
  | |  | |    || ||      ||||||| | |||| | ||| || |||   ||| ||| ||  |   ||| | |  | || |   ||  | |||  ||||||||||||||||||||||||||| |||| || |||||||| |||||||
--ttttctagaaaatatttgcaaaattgttaaagcaataat-ctctaactctgactatctgagtatgacgatgaagaagatgacagttattcatatttctcagGTTAATGCTGCTAATGAGCGAATGCTAGGAGGTGGAGGTGTAGATGGAG
















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|60346456|gb|DN213429.1|DN213429
EST:     CGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAGCT
genomic: CGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGAT-G-G--
EST: gi|60350894|gb|DN217867.1|DN217867
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAGCT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGAT-G-G--
EST: gi|60400550|gb|DN233357.1|DN233357
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAGCT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGAT-G-G--
EST: gi|149058791|gb|EE156812.2|EE156812
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAGCT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGAT-G-G--
EST: gi|71760661|gb|DR958598.1|DR958598
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAGCT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGAT-G-G--
EST: gi|211491111|gb|FL180880.1|FL180880
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGT
EST: gi|211488222|gb|FL180860.1|FL180860
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTT
EST: gi|76284272|gb|DV023840.1|DV023840
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAGCT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGAT-G-G--
EST: gi|71775282|gb|DR973160.1|DR973160
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAGCT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGAT-G-G--
EST: gi|78118087|gb|DV536474.1|DV536474
EST:     ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATC                         GTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAGCT
genomic: ACAAGGGCGACATCACCCTCTGGTCCGTCGACTGCGCCACCGACGCCATCgtacgctctt ... gttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGAT-G-G--


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatctctgtatgtgataaaaaactgagggatgtaactggcgtttgttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAG
                              atgtaac  putative branch site (score: 3)
                                          tttgtttt  putative PPT
         tatgtgataaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtatttgtctctaattcgtcccttgttaatgaatattgctcaaaatctctgtatgtgataaaaaactgagggatgtaactggcgtttgttttggcagGTTAATGCTGCTAATGAGCGAATGTTAGGTGGCGGAGGTGTTGATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA