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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatatttagttttgctgggcaaactttcagtataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA

Basic information

species Zea mays
transcript GRMZM2G047404_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047404_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 3'ss of exon 2
gtgaatatttagttttgctgggca---------aactttcagtataaacacagtgcatca--aaattaa-tgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA
|| | ||| |   | |    |  |         ||| |||  || | |   | ||||  |  ||   || | |||   |||| ||| ||||  |||||   |||||||||||||| ||||| ||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |
gtaattatatttctctataagatacatcgtgacaacattcgatacacatgtattgcactatgaagccaactattgtaactgtccttatttc--agCTTGCTGCTATCCTTCCTCTCGCTATGGTCCACACCATGGGCAATCTTTTCACGAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATCA

upper sequence: GRMZM2G047404_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27053 (Selaginella moellendorffii), 3'ss of exon 2
gtgaatatttagttttgctgggcaaactttca---gtataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA
           || | |  |   ||| | ||    || |  |   ||    ||||| ||        ||   || ||  |||  || |  |||| ||| | || || ||  | || || |||||||| ||||| || || ||||||||||||||||||||||| ||||| ||||| || || || |
-----------gtatcgtcgtagaaattgtcgtttgtgtcgatcgagcatctcaaacttt-------tgtccttgtttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCGTTTACTCACACAATCA

upper sequence: GRMZM2G047404_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 2
gtgaatatttagttttgctgggcaaactttcagt-ataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA
           || | |  |   ||| | ||  |  |  | |  | |||||   |  ||| |||    ||||     |||  || |  |||| ||| | || || ||  | || || |||||||| ||||| || || ||||||||||||||||||||||| ||||||||||| || || || |
-----------gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttgtccttgtttc---ttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA

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|22521317|gb|BU080128.1|BU080128
EST:     TCATGTGGATTACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|88746767|gb|DY530908.1|DY530908
EST:     TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|21891481|gb|BQ744694.1|BQ744694
EST:     TCATGTGGATTACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|87156219|gb|DY401008.1|DY401008
EST:     TCATGTGGATTACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGGAATCTTT
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTT
EST: gi|26559240|gb|CA831475.1|CA831475
EST:     TCATGTGGATTACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA
                        aattaat  putative branch site (score: 3)
                                      ctgttcttgtttccc  putative PPT
                   atcaaaattaatgtt  TA-rich tract