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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtcttcctttctgttctgtagtaaaccataccgggaaaatgcaatttttgattcctgcagggttgttcctatttgggctgaattttgttttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAGCAATCCAAGCAACTGAAGATCAGCTGCAACCTAAACAATGCTGCCTGCA

Basic information

species Zea mays
transcript GRMZM2G096585_T05
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 9
--gtggtcttcct-ttctgttctgtagtaaaccataccgggaaaatgcaatttttgattcctgcagggttgt--tcctatttgggctga-attttgt---tttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAGCAATCCAAGCAACTGAAGATCAGCTGCAACCTAAACAATGCTGCCTGCA
   |||  | | | || ||||    | |    || |     ||  |    |      || ||      |  |  |||  |   | ||||   | | |   ||| ||| |||||||| || | ||||||||| ||||  || || || |||||||||||||| |||||||||||||||||| | | ||||||| | ||||||||||||||||
gtatggcatgcttcttttgttgaacacttgttcaaataactaatctttcgtcaagattttctttgttttcataatcccttactgactgatgatctatctattttattccagGCTGCAAAATTCATTGAGTATGACAGCTCATTTAGCGAAGATGAGAAGAAACAATCCAAGCAACTGAAGGTTACCTGCAACTTGAACAATGCTGCCTGCA
















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|32931241|gb|CF036053.1|CF036053
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTA
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTA
EST: gi|166616885|gb|EG290584.1|EG290584
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTACATTGAGTACGACAC
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACAC
EST: gi|211294948|gb|FL187036.1|FL187036
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTACAT-GAGTACGACACTTCGTTCAGTGAAGATGAGAAGA
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGA
EST: gi|5901160|gb|AW042260.1|AW042260
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTTCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
EST: gi|211292817|gb|FL187031.1|FL187031
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAG
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAG
EST: gi|33094689|gb|CF054683.1|CF054683
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTAC
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTAC
EST: gi|32934317|gb|CF039129.1|CF039129
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTAC
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTAC
EST: gi|8383116|gb|BE055999.1|BE055999
EST:     CAAATATACTAGAGCTTCCAAGCGATACGAGAAG                         GCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
genomic: CAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
EST: gi|211292815|gb|FL187029.1|FL187029
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
EST: gi|6307877|gb|AW163844.1|AW163844
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTTCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
EST: gi|67012006|gb|CO440755.1|CO440755
EST:     C-TTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAG
EST: gi|211294949|gb|FL187037.1|FL187037
EST:     CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAG                         GCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAG
genomic: CATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc ... ttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgattcctgcagggttgttcctatttgggctgaattttgttttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAGCAATCCAAGCAACTGAAGATCAGCTGCAACCTAAACAATGCTGCCTGCA
                                           ttttaat  putative branch site (score: 3)
                                      ttttgtttt  CT-rich tract
                                  tgaattttgttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtcttcctttctgttctgtagtaaaccataccgggaaaatgcaatttttgattcctgcagggttgttcctatttgggctgaattttgttttaattgcagGCTGCCAAGTACATTGAGTACGACACTTCGTTCAGTGAAGATGAGAAGAAGCAATCCAAGCAACTGAAGATCAGCTGCAACCTAAACAATGCTGCCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC