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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccagatccgcagcgcgcccgcgcgattccgtccgcccgacgcgagttcccctgtgtattttttttgtgatgatttttttgacctctttgcctggtctagGGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACGACGGCATGGACGACGACG

Basic information

species Zea mays
transcript GRMZM2G103430_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g06130.3 (Oryza sativa), 3'ss of exon 1
------------------------------------------------cccagatccgcagcgcgcccgcgcgattc------cgtccgcccgacgcgagttcccctgtgtattttttttgtgatgatttttttgacctctttgcctggtctagGGTT---AGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACGACGGCATGGACGACGACG------
                                                   ||||| | ||| ||| ||  | ||||       ||      ||   | ||| |  | |||   ||  | ||   |  |||         |||  || ||   |||||   |||||| |   |  | |||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||  ||||||||||||||      
gtaccgatttattttatttttttttcaattttttgatcctgatgatgcgttagatctgtagcacgcgcgttcaattcgtctcttgttttgaggatttgtgttgctttttgtgggttggtggtttaggatttacgttttcttttatcttgttgggggtttctagGGTTAGGGTTTTGGGATGGCGGATCGGCAGCAGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACGACATCATGGACGACGACGACGGGT

upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 1
cccagatccgcagcgcgcccgcgcgattcc--gtccgcccgacgcgagttcccctgtgtattttttttgtgatgatttttttgacctctttgcctggtctagGGTT---AGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACGACGGCATGGACGACGACG------
            |||||  |      |  |  ||      ||   | ||| |  | |||   ||  | ||   |  |||         |||  || ||   |||||   |||||| |   |  | |||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||  ||||||||||||||      
-----------cgcgcgttcaattcgtctcttgttttgaggatttgtgttgctttttgtgggttggtggtttaggatttacgttttcttttatcttgttgggggtttctagGGTTAGGGTTTTGGGATGGCGGATCGGCAGCAGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACGACATCATGGACGACGACGACGGGT

upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------------------cccagatccgcagcgcgcccgcgcgattccgtccgcccgacgcgagttcccctgtgtattttttttgtgatgatttttt--tgacctctt--tgcctggtctagGGTTAGGGTTTGC-TGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACG------ACGGCATGGACGACGACG
                                                             |  || | | |  |  |  |  |   ||   |  |      ||| | | |  |  | ||    ||| ||||  ||||||  |||  |  |  || |||||       ||||||| |  | | || |||||| || ||||||| ||||||||||||||||||||||||||||||||||||||||||||      ||| ||||||||||||| 
gtgagcgcacctcctccctctagctcttcctcctctttcttctctatcttttttccttaacctaagcttctcctctagatc-tggagttttttttgggttttgcgggattcttttgggatgggatttctgatttttttttggtgatgtggtggtggctggttcgtttctagGGTTAGGGTTTTGGGGATGTCCGACCGGCAGCAGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACGACAACGACGTCATGGACGACGAC-

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|211409108|gb|FK978703.1|FK978703
EST:     GGCGGCCCCCAAAAGCCAAATTCCCCAGCCCACACCACCTCCACACTCCA                         GGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAACCG
genomic: GGCGGCCCCCAAAAGCCAAATTCCCCAACCCACACCACCTCCACACTCCAgtaagcaccc ... cctggtctagGGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCG
EST: gi|211409115|gb|FK978710.1|FK978710
EST:     GGCGGCCCCCAAAAGCCAAATTCCCCAGCCCACACCACCTCCACACTCCA                         GGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAACCG
genomic: GGCGGCCCCCAAAAGCCAAATTCCCCAACCCACACCACCTCCACACTCCAgtaagcaccc ... cctggtctagGGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCG
EST: gi|211411663|gb|FK978721.1|FK978721
EST:     GGCGGCCCCCAAAAGCCAAATTCCCCAGCCCACACCACCTCCACACTCCA                         GGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAACCG
genomic: GGCGGCCCCCAAAAGCCAAATTCCCCAACCCACACCACCTCCACACTCCAgtaagcaccc ... cctggtctagGGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCG
EST: gi|211409116|gb|FK978711.1|FK978711
EST:     GGCGGCCCCCAAAAGCCAAATTCCCCAGCCCACACCACCTCCACACTCCA                         GGTTAGGGTTTGCTGTCGGCGAT
genomic: GGCGGCCCCCAAAAGCCAAATTCCCCAACCCACACCACCTCCACACTCCAgtaagcaccc ... cctggtctagGGTTAGGGTTTGCTGTCGGCGAT
EST: gi|211411666|gb|FK978724.1|FK978724
EST:     GGCGGCCCCCAAAAGCCAAATTCCCCAGCCCACACCACCTCCACACTCCA                         GGTTAGGGTTGGCTGTCGGCGATGTC
genomic: GGCGGCCCCCAAAAGCCAAATTCCCCAACCCACACCACCTCCACACTCCAgtaagcaccc ... cctggtctagGGTTAGGGTTTGCTGTCGGCGATGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcccctgtgtattttttttgtgatgatttttttgacctctttgcctggtctagGGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACGACGGCATGGACGACGACG
                               ttttgac  putative branch site (score: 3)
                                     cctctttgcct  CT-rich tract
           tattttttttgtgatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccagatccgcagcgcgcccgcgcgattccgtccgcccgacgcgagttcccctgtgtattttttttgtgatgatttttttgacctctttgcctggtctagGGTTAGGGTTTGCTGTCGGCGATGTCGGATCGGCAGCCGTCGGAGGAGCCGGAGGAGCAGGTGGACCTGGAGGGGGACGACGACGGCATGGACGACGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA