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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcgccctctccgcccaggagagagcgacgcagggttctaagagaaatataactgtcaatgattggattgggactctaagacacactgatattctgacagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTATCTCATGGTTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCGGACACCT

Basic information

species Zea mays
transcript GRMZM2G036872_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036872_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 14
gtcgccctctccgcccaggagagagcgacgcagggttctaagagaaatataactgtcaatgattggattgggact-ctaa-gacacactgatattctg----acagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTATCTCATGGTTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCGGACACCT
       | |      | |  |  ||  ||  | ||  |     |  |  ||     ||  ||   |||  | |  || | | ||||   |  |||||    |||| || |||   |  |  |||| || |||||||||||||| ||||| |||||| ||||||||||||||||||| |||||||| ||||| |||  |||| |||
------gtttatagaaaagcaaaggcaccgatgagtaattgtctacttgcaatgtaaaaaaatcccatttcgtccactgatggcacaacaacgttctgtgtgacagCAGGGCCCCGCAGGTGCATCGCATTGGAGAAGCATCAAGCAGCACGTGCTACCTCATGGTTCTTCAAGGCCCTTCTCCCGGAAGCACTCCATGGACGCCT

upper sequence: GRMZM2G036872_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os07g46450.1 (Oryza sativa), 3'ss of exon 20
gtcgccctctccgcccaggagagagcgacgcagggttctaagagaaatataactgtcaatgattggattgggact-ctaa-gacacactgatattctg----acagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTATCTCATGGTTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCGGACACCT---
         |      | |  |  ||  ||  | ||  |     |  |  ||     ||  ||   |||  | |  || | | ||||   |  |||||    |||| || |||   |  |  |||| || |||||||||||||| ||||| |||||| ||||||||||||||||||| |||||||| ||||| |||  |||| |||   
---------tatagaaaagcaaaggcaccgatgagtaattgtctacttgcaatgtaaaaaaatcccatttcgtccactgatggcacaacaacgttctgtgtgacagcagGGCCCCGCAGGTGCATCGCATTGGAGAAGCATCAAGCAGCACGTGCTACCTCATGGTTCTTCAAGGCCCTTCTCCCGGAAGCACTCCATGGACGCCTCGT
















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|37391484|gb|CF632985.1|CF632985
EST:     TTTCTGTAATCAAGAGAAGCAAAGAAATGAG                         GAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
genomic: TTTCTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... attctgacagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
EST: gi|18965228|gb|BM661464.1|BM661464
EST:     GATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAG                         GAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
genomic: GATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... attctgacagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
EST: gi|60356361|gb|DN223334.1|DN223334
EST:     GCTTTCTGTAATCAAGAGAAGCAAAGAAATGAG                         GAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
genomic: GCTTTCTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... attctgacagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
EST: gi|60337955|gb|DN204928.1|DN204928
EST:     GATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAG                         GAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
genomic: GATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... attctgacagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
EST: gi|16926041|gb|BM079109.1|BM079109
EST:     CAAGAGAAGCAAAGAAATGAG                         GAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
genomic: CAAGAGAAGCAAAGAAATGAGgttagctgtt ... attctgacagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
EST: gi|18167769|gb|BM337609.1|BM337609
EST:     GATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAG                         GAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA
genomic: GATTTGATAGGAGCGTTGCTTTCTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... attctgacagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatataactgtcaatgattggattgggactctaagacacactgatattctgacagGAGAGCCTGCCGAGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTATCTCATGGTTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCGGACACCT
                                      cactgat  putative branch site (score: 3)
            aatgatt  TA-rich tract