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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataagtcgtggctcgtgggttgccatttggaaaagggtgggtttttttttgttcacttgaatgatgtgttgattttctgtttcctgtcactgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG

Basic information

species Zea mays
transcript GRMZM5G834205_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G834205_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 2
-------cataagtcgtggctcgtgggttgccatttggaaaagggtgggtttttttttgttcacttgaatgatgtgttgattttctgtttcctgtcactgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG
        | ||||  |||||| ||| ||||||| ||||||     ||||  |||| ||| |  |||||||   | || || ||      ||||| |||| |||||||||||||||||||||||||||| |  ||||||||| | |||| ||||||||||||| ||||||||| | ||||||||||
tcctttagacaagttatggctcatggtttgccatatggaaa-----gggtgcttttatgtcc--ttgaatggcctatttatgtttatcaacctgttactgtcaccagGAAAGCGAAGGATGTGATCAAGCCGATAAAGAAGTATTTAGGTAGCAGGAGCAAGAACACTCAACTTTATGCTGTTATG
















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|89761509|gb|DY689496.1|DY689496
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|71421501|gb|DR805467.1|DR805467
EST:     TTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGA
genomic: TTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagG-AAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGA
EST: gi|50325447|gb|CO520573.1|CO520573
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|78107223|gb|DV525641.1|DV525641
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|93017403|gb|EB642923.1|EB642923
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|149059924|gb|EE157051.2|EE157051
EST:     GCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|71421504|gb|DR805468.1|DR805468
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|50339160|gb|CO534286.1|CO534286
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|71326005|gb|DR799685.1|DR799685
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|71320277|gb|DR796887.1|DR796887
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|78107222|gb|DV525640.1|DV525640
EST:     ATTGGGCAAAG-ACATCGAAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATA-GGAGCAGGGA
genomic: ATTGGGCAAAGAACATCG-AAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCA-GGA
EST: gi|44682243|gb|CK787291.1|CK787291
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCT--                         G---GCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|148952813|gb|EC898805.2|EC898805
EST:     GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
EST: gi|71326004|gb|DR799684.1|DR799684
EST:     GATTGGGCAAAGACCATCGAAATTTGCGAGCTCGTGGCGCAGGATCCTGG                         GAAAGCGAGGGATGTGATCTAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG
genomic: GATTGGGCAAAGAACATCGAAATCTGCGAGCTCGTGGCGCAGGATCCTGGgtatgcttgc ... ctgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgttcacttgaatgatgtgttgattttctgtttcctgtcactgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG
                      tgttgat  putative branch site (score: 4)
                        ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataagtcgtggctcgtgggttgccatttggaaaagggtgggtttttttttgttcacttgaatgatgtgttgattttctgtttcctgtcactgccaccagGAAAGCGAAGGATGTGATCAAGTCTGTAAAGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT