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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatatactacgtcaacttccactacacccagtactccgtttcagcttcagttggacacttacattcaaatcaacattatcaaatcaaaatgtatttttttagatatattagaaagtgtttggaactaactgtggaaagggggaaaaactgtagGAGGCTATGACAAGGAGGAGAAGGCGGCTAGAGCTTACGACCTCGCCGCGCTCAAGTACTGGGGGCCTACAACCACGACCAACTTCCCG

Basic information

species Zea mays
transcript GRMZM2G139082_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139082_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g44750.1 (Oryza sativa), 3'ss of exon 4
gtacgtatatactacgtcaacttccactacacccagtactccgtttcagcttcagttggacacttacattcaaatcaacattatcaaatcaaaatgtatttttttagatatattagaaagtgtttggaactaactgtggaaagggggaaaaactgtagGAGGCTATGACAAGGAGGAGAAGGCGGCTAGAGCTTACGACCTCGCCGCGCTCAAGTACTGGGGGCCTACAACCACGACCAACTTCCCG
                                           | ||  | | | ||| |     ||||  | ||  |  |||   | | |   | | ||   || | |    | || | |   || ||  |  || || |      ||||  |  |||||| ||||| |||||||||||||| || |||||||||||||||||||| || ||||||||||| || || |||||||| |||||||| 
----------------------------------------gtatgtcgtcattatttgca-----acatctatat--atcttaattagttagtttcttttccattcgttcaccttgagacttactgtaaa-agttgggggattaaacaaaactttcagGAGGTTATGATAAGGAGGAGAAGGCCGCAAGAGCTTACGACCTCGCCGCCCTAAAGTACTGGGGTCCAACCACCACGACGAACTTCCCT

upper sequence: GRMZM2G139082_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
gtacgtatatactacgtcaacttccactacacccagtactccgtttcagcttcagttggacacttacattcaaatcaacattatcaaatcaaaatgtatttttttagatatattagaaagtgtttggaactaactgtggaaagggggaaaaactgtagGAGGCTATGACAAGGAGGAGAAGGCGGCTAGAGCTTACGACCTCGCCGCGCTCAAGTACTGGGGGCCTACAACCACGACCAACTTCCCG
                                    | ||||  |  | |||  ||  |  |  ||   || |||     || || | |    |  ||   |||| |   | ||      | |||         | ||                ||||| || |||||   |||||||||||| || ||||||||||| || || || |||||||||||||||||||| || || || ||||| |||
------------------------------------tcctccagtgta-cttaggtgagtaatcta---tcgaattt---ttctcgattgtggagctaaacttttggtggttttcttttctttttttcttgcgttttg---------------cgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG

upper sequence: GRMZM2G139082_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
----------------------gtacgtatatactacgtcaacttccactacacccagtactccgtttcagcttcagttggacacttacattcaaatcaacattatcaaatcaa-aatgtatttttttagatatattagaaagtgttt---------ggaactaactgtggaaaggg-------ggaaaaactgtagGAGGCTATGACAAGGAGGAGAAGGCGGCTAGAGCTTACGACCTCGCCGCGCTCAAGTACTGGGGGCCTACAACCACGACCAACTTCCCG
                      ||   | |  |     |    |  | ||      | |  |||||    |  || |   |    ||    |    |  || | ||| |  |   | |||| ||   |   ||   ||   | | |||         ||| ||||   |     ||        |        ||||| || |||||   |||||||||||| || ||||||||||| || || || |||||||||||||||||||| || || || ||||| |||
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggt--acttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG

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|148960407|gb|EE153669.2|EE153669
EST:     GCAAAGGACGGCAAGTCTACCTAG                         GAGGCTATGACAAGGAGGAGAAGGCGGCTAGAGCTTACGAACTCGCCGCG
genomic: GCAAAGGACGGCAAGTCTACCTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagatatattagaaagtgtttggaactaactgtggaaagggggaaaaactgtagGAGGCTATGACAAGGAGGAGAAGGCGGCTAGAGCTTACGACCTCGCCGCGCTCAAGTACTGGGGGCCTACAACCACGACCAACTTCCCG
                        aactaac  putative branch site (score: 1)
     tatattagaaa  TA-rich tract