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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgggatttacaatctaagttgtatcatcaccatttttccttctagaacttctggatctgatgtcatgcactacagactcatgtttgtgaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAAGGAGACCGCCACCCTTATTCTATGTTAGATTGTGTGGCACAGCGTGAAA

Basic information

species Zea mays
transcript GRMZM5G877316_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G877316_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 4
cattgggatttacaatctaagttgtatcatcaccatttttccttctagaacttctggatctgatgtcatgcact-acagactcatgtttgtgaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGA---AGAAGGAGACCGCCACCCTTATTCTATGTTAGATTGTGTGGCACAGCGTGAAA
      ||| | |||  | | ||   |  |     ||     | || |||   |      ||    |   |||| | |     || ||||  ||| ||||||| || ||  ||||||| |||||||||||||||||  ||||||||||   ||||||||| || ||||| |||||| |  | |||||||  || |||||||   
-tgaaagatgtgcaaaatgaattaagtactggagtttcaatttccttgaataacccttgttgtcaacgaacacttaaatgtaaatatttgaaaaactgcagGTTGTATTCATTGGAGGGCGCACTCAGCCTGGCACAATAAAACCTGAGGAAGAAGGAGAGCGTCACCCCTATTCTGTACTTGATTGTGCAGCGCAGCGTG---
















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|18662176|gb|BM501785.1|BM501785
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|26457615|gb|CA829198.1|CA829198
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|32826208|gb|CD965886.1|CD965886
EST:     TTGAGTCTTCCGGCCTCAACTTCTCACGTTACGGTGACGCC-TTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|78108789|gb|DV527206.1|DV527206
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|76912266|gb|DV164646.1|DV164646
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|22521606|gb|BU080417.1|BU080417
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GGGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|61117466|gb|DN558427.1|DN558427
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|71428140|gb|DR809190.1|DR809190
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|19436862|gb|BM953272.1|BM953272
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|23199654|gb|BU582219.1|BU582219
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGG-GACACCTTTTTTGAG                         G-GGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|19057519|gb|BM736186.1|BM736186
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|87153853|gb|DY398642.1|DY398642
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|18655178|gb|BM499983.1|BM499983
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|19057686|gb|BM736353.1|BM736353
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|19436861|gb|BM953271.1|BM953271
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|32823889|gb|CD963611.1|CD963611
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
EST: gi|78084825|gb|DV513218.1|DV513218
EST:     TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAG                         GTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA
genomic: TTGAGTCTTCCGACCTCAACTTCTCACGTTACGGTGACACCTTTTTTGAGgtacggccag ... gaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaacttctggatctgatgtcatgcactacagactcatgtttgtgaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAAGGAGACCGCCACCCTTATTCTATGTTAGATTGTGTGGCACAGCGTGAAA
            atctgat  putative branch site (score: 4)
                                            tgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgggatttacaatctaagttgtatcatcaccatttttccttctagaacttctggatctgatgtcatgcactacagactcatgtttgtgaaaatgcagGTGGTTTTTGTTGGAGGACGCACTCAGCCTGGCACTGTAAAACCTGAAGAAGGAGACCGCCACCCTTATTCTATGTTAGATTGTGTGGCACAGCGTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA