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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagcattctttatcattaattttggttacttcttcagcagtggatcttcaatatgtgttacctttttgtgaaatttgaccttgaccttttctgttccagCTGCTGGACAGGGTGTTCAACATTCTACGTGAGAACAACCCAGATCTTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGG

Basic information

species Zea mays
transcript GRMZM2G080048_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080048_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g48300.1 (Oryza sativa), 3'ss of exon 6
gcagcattctttatcattaattttggttacttc--ttcagcagtggatcttcaatatgtgttacctttttgtgaaatttgaccttgaccttttctgttccagCTGCTGGACAGGGTGTTCAACATTCTACGTGAGAACAACCCAGATCTTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGG
 || |||| |  | ||  ||     || |         ||||  | ||   |||  |    ||  |   |||||||       |||    ||| |||| ||||| |||| ||| |||||||| ||||| ||||| ||||| |||||||||||||| || || || || || || |||||||| ||||| |||||| | ||||
-caacattgtgaaacagaaacaactgtcatccagaactagcacagaatgaccaaattactgtag-tgcgtgtgaaaacctgatttgggtatttttgttgcagCTTCTGGGCAGAGTGTTCAATATTCTGCGTGAAAACAATCCAGATCTTGCTGGAGACAGACGCAGAACTGTCATGAGGCCGCCACAGGTTCTTCGAGAGG
















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|26455990|gb|CA827573.1|CA827573
EST:     TCCCTACATACCCTTGGGAGGGAACTGATCGGGATTATAAATATGAAGAG                         CTGCTGGACAGGGTGTTCAACATTCTACGTGAGAACAACCCAGATCTTGCT
genomic: TCCCTACATACCCTTGGGAGGGAACTGATCGGGATTATAAATATGAAGAGgtgcttaaat ... tctgttccagCTGCTGGACAGGGTGTTCAACATTCTACGTGAGAACAACCCAGATCTTGCT
EST: gi|6194479|gb|AW146583.1|AW146583
EST:     TCCCTACATACCCTTGGGAGGGAACTGACCGGGATTATAAATATGAAGAG                         CTGCTGGACAGGGTGTTCAACATTCTTCGTGAGAACAACCCAGATCTTGCT
genomic: TCCCTACATACCCTTGGGAGGGAACTGATCGGGATTATAAATATGAAGAGgtgcttaaat ... tctgttccagCTGCTGGACAGGGTGTTCAACATTCTACGTGAGAACAACCCAGATCTTGCT
EST: gi|19822348|gb|BQ048372.1|BQ048372
EST:     TCCCTACATACCC-TGGGAGGGAACTGATCGGGATTATAAATATGAAGAG                         CTGCTGGACAGGGTGTTCAACATTCTACGTGAGAACAACCCAGATCTTGCT
genomic: TCCCTACATACCCTTGGGAGGGAACTGATCGGGATTATAAATATGAAGAGgtgcttaaat ... tctgttccagCTGCTGGACAGGGTGTTCAACATTCTACGTGAGAACAACCCAGATCTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcaatatgtgttacctttttgtgaaatttgaccttgaccttttctgttccagCTGCTGGACAGGGTGTTCAACATTCTACGTGAGAACAACCCAGATCTTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGG
                                  ccttgac  putative branch site (score: 4)
                                        ccttttctgttcc  CT-rich tract
                  tttttgtgaaattt  TA-rich tract