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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatctttttttacctttttctgttcacatataatcttgaatctgttttttatgttgttgatagatggccatcttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT

Basic information

species Zea mays
transcript GRMZM2G139038_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 2
gtaattatc--tttttttacctttttctgttcac-atataatcttgaatctgttttttatgttgttgatagatggccatcttttcta---cagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT
|||| | |   |||      || ||| ||||  | |  ||  ||  || || |  |      |||  |  |||   ||| ||   ||   |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||| |||||  |||||||||| 
gtaactgttgatttgacgctctatttttgtttgccaagtatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTAC
















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|67025976|gb|CO454725.1|CO454725
EST:     CAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGTGTACTCCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAGgtaattatct ... ttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|89760369|gb|DY688806.1|DY688806
EST:     CAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAGgtaattatct ... ttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataatcttgaatctgttttttatgttgttgatagatggccatcttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT
                           tgttgat  putative branch site (score: 4)
                                        ccatcttttct  putative PPT
           aatctgttttttat  TA-rich tract