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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgtttcagccggacctttgttctgccctggaatatctgatcttgtattgttaatcacctttatttctctatctgttttctgatcaattattttaattgccagCCTCTCCAAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTGCCGAGTCGTCTGCATTTCTAGCATATGTCAAGCCAAGCACCCCAGCCAC

Basic information

species Zea mays
transcript GRMZM2G020081_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020081_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 5
gtaagatgtttcagcc--ggacctttgttctgccctggaatatctgatcttgtattgttaatcacctttatttctctatctgttttctgatcaattattttaattgccagCCTCTCCAAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTGCCGAGTCGTCTGCATTTCTAGCATATGTCAAGCCAAGCACCCCAGCCAC
|||||    || ||||    ||| ||    |   |||   || | ||||    | | | ||  |   |  |||||     |  |  ||      ||  ||| || |||||| |||||  ||  |  ||||||||| || ||||| |||||| |||||||||| ||||| ||||| |||||||| ||||| ||| ||||||||||| | ||
gtaagtatcttgagccttaaaccatttcctttagctgatttagcagatcccccaat-tgaagaa---tagtttctaaggtttatgcct------ttgcttttat-gccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC
















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|32839851|gb|CD979532.1|CD979532
EST:     AGAAAAGATGGAGGGTGTTCCAGGCTCTGCCCTAGATGCCAGTAAAAAAT                         CCTCTCCAAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTG
genomic: AGAAAAGATGGAGGGTGTTCCAGGCTCTGCCCTAGATGCCAGTAAAAAATgtaagatgtt ... taattgccagCCTCTCCAAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTG
EST: gi|32839850|gb|CD979531.1|CD979531
EST:     AGAAAAGATGGAGGGTGTTCCAGGCTCTGCCCTAGATGCCAGTAAAAAAT                         CCTCTCCAAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTG
genomic: AGAAAAGATGGAGGGTGTTCCAGGCTCTGCCCTAGATGCCAGTAAAAAATgtaagatgtt ... taattgccagCCTCTCCAAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaatcacctttatttctctatctgttttctgatcaattattttaattgccagCCTCTCCAAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTGCCGAGTCGTCTGCATTTCTAGCATATGTCAAGCCAAGCACCCCAGCCAC
                                          ttttaat  putative branch site (score: 3)
                                       ttatttt  CT-rich tract
                           ttttctgatcaattat  TA-rich tract