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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctcgaaagcttcaattatattactcaaaaacccttttaagcttgcatttttcttcctttagttgtcgaacgttcttaactctattattctggtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAATAATCAGGCCCTGGGCGG

Basic information

species Zea mays
transcript GRMZM2G168506_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 4
gtacctcgaaagcttcaattatattactcaaaaacccttttaagcttgcatttttcttcctttagttgtcgaacgttcttaactctattattctggtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAATAATCAGGCCCTGGGCGG
||| |   || || | ||  ||  ||    ||||    | ||      |||||||     | || |  |  || | | ||| |  |||  | |    ||| | ||| ||||| ||| ||||||| |||||||| || |||||||| ||||| ||||| || ||||| || ||||||||||||||||||||||| || || || ||
gtatccgaaatgcct-aaccattctaggttaaaatttctcta---cctcattttt-----tgtaatcatt-aatggtattatcattatcttgcc--catgtttagATAATGGCGAATCCATTCAAATATTACATTATCAGAATGGCGAGAAGTATGAGCCACACTATGATTACTTCCATGACAAAAATAATCAAGCTCTTGGAGG

upper sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ23963 (Selaginella moellendorffii), 3'ss of exon 5
gtacctcgaaagcttcaattatattactcaaaaacccttttaagcttgcatttttcttcctttagttgtcgaacgttcttaactctattattctggtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAATAATCAGGCCCTGGGCGG
                                           | |    ||| | ||||   ||||   ||  | | ||| |    ||    | || |    |||||| ||||| ||||| ||  |  ||| |||| ||  ||| ||||||||||| ||||||||||||||||| || || ||| | || || || || || ||
-------------------------------------------gttctagtttcttttcca--agtttatga--ggttttatcc---ttggatttgtttttctagAGAACGGTGAGGCCATCCAAGTCCTACGCTACGAGTTTGGCGAGAAATATGAGCCCCACTACGACTACTTTCACGATAAATACAACCAAGCTCTCGGTGG

upper sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ21588 (Selaginella moellendorffii), 3'ss of exon 4
gtacctcgaaagcttcaattatattactcaaaaacccttttaagcttgcatttttcttcctttagttgtcgaacgttcttaactctattattctggtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAATAATCAGGCCCTGGGCGG
                                   |   ||    |||||| ||| || |     || ||       |||   | | || ||||         |||||| ||||| ||||| ||  |  ||| |||| ||  ||| ||||||||||| ||||||||||||||||| || || ||| | || || || || || ||
--------------------------------gttctagtttcttttgcatatttttttccaagtttatc-------cttgggtttgtttttct---------agAGAACGGTGAGGCCATCCAAGTCCTACGCTACGAGTTTGGCGAGAAATATGAGCCCCACTACGACTACTTTCACGATAAATACAACCAAGCTCTCGGTGG

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|50334167|gb|CO529293.1|CO529293
EST:     AGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|4647604|gb|AI622679.1|AI622679
EST:     GAGGAGAGGATATCTGCTTGG-CATTTCTTCCACCAG                         AGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: GAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|12972561|gb|BG268043.1|BG268043
EST:     CATTTCTTCCACCAG                         AGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: CATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|83278553|gb|DV942561.1|DV942561
EST:     TAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: TAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcttcctttagttgtcgaacgttcttaactctattattctggtatgctcagAGAATGGTGAAGCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAATAATCAGGCCCTGGGCGG
                          tcttaac  putative branch site (score: 2)
                            ttaactctattatt  TA-rich tract