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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtccactcccctcattaccctggcccccgcccccctccctcaaacgtcttccagatcccggtcggtctctgactctcagtggttcgcgtcgctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC

Basic information

species Zea mays
transcript GRMZM2G172101_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 1
gtaagtgtccactcccctcattaccctggcccccgcccccctccctcaaacgtcttccagatcccggtcggtctctgactctcagtggttcgcgtcgctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC
                         ||   || | |||   |   || |||  ||| |||||||    ||||| ||||  |  ||   |   | ||   || ||||||||||||||||| ||||| ||||||||||||||||||   ||||||||| | || ||||||||||| || 
-------------gtaagagaggggcttctcctcacccggattgatcgaac-ccttgcagatccg---cggtccctgatccctagctat--acttcttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT

upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g37837.2 (Oryza sativa), 3'ss of exon 1
gtaagtgtccactcccctcattaccctggcccccgcccccctccctcaaacgtcttccagatc--ccggtcggtctctgactctcagtggttcgcgtcgctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC
||||| |        | || | || |   |||  ||         || |||  ||| |  |||  |||  |  || |||||    |||  | |  ||    || |||||||| |||||||| ||||| ||||||||||||||||||   ||||||||| | || ||||||||||| || 
gtaagagagagggggcttc-tcactc--acccgggcggga-----tcgaaccccttgcgaatccgccgtcccttccctgaccactagttatgcttgtt--cgccgcagGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
















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|211021857|gb|FL368551.1|FL368551
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
EST: gi|211054847|gb|FL421737.1|FL421737
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
EST: gi|18171951|gb|BM347339.1|BM347339
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
EST: gi|148937654|gb|EC881846.2|EC881846
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
EST: gi|37421408|gb|CF648402.1|CF648402
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
EST: gi|18174283|gb|BM349671.1|BM349671
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
EST: gi|148931370|gb|EC874280.2|EC874280
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
EST: gi|28985482|gb|CB350662.1|CB350662
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
EST: gi|18164364|gb|BM334203.1|BM334203
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAA                         GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACAAGGCATGGCGCGAAAgtaagtgtcc ... gctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttccagatcccggtcggtctctgactctcagtggttcgcgtcgctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC
                     ctctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtccactcccctcattaccctggcccccgcccccctccctcaaacgtcttccagatcccggtcggtctctgactctcagtggttcgcgtcgctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA