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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgtaaataagcagaagctttttcctcttgctgtgtaactctaatgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT

Basic information

species Zea mays
transcript GRMZM2G063253_T08
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 5
cctgtaaataagcagaagctttttcctc--ttgctgt-gtaactctaatgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT
   |||| ||       | |||    |   |  || |  |   ||  |    | |     ||| |||||| ||  |||||||| ||| ||||||    || |||||||||||||||||||||||||||||||||| || ||||||||| |  | ||||| |||||||| || |||||||||||||| || || ||||| || |
---gtaactatttttttgttttccttttgatcactattatggatcacaattttgtagtactctattttgttgttggtttctgtcatccttaaccagctattagATGACAAACACTATCCAGAAGAAGTTCAAGGTTTCTTCAACCCAATTATTATACCAATCTTGCCCCTATCAATCACTGACCCTCTTCCTTATTGGTCCAT

upper sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
cctgtaaataagcagaagctttttcctcttg-ctgtgtaactctaatgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgt--tcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT
  | |    |     ||||||| |     ||  ||| |   | |        || | |    |||| |  |  |     ||   ||| |   ||     | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || || ||| ||   ||||||||  ||  ||| || |
--tattg-cacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT

upper sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
cctgtaaataagcagaagctttttcctcttg-ctgtgtaactctaatgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgt--tcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT
  | |    |     |||||||       || |||| |   | |        || | |    |||| |     |      |   ||| |   ||  |  | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || || ||| ||   ||||||||  |   |||||| |
--tattg-cacttgaaagctttacaaaggtggctgtctgcttttttcattcctgggctatcattttttatctgggcgtcttgtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT

upper sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 5
cctgtaaa-taagcagaagctttttcctcttgctgtgtaactctaatgcatttgagt---ttctgttttg---tggtcagtttctgtaatctttaaccgttcat---cagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT
   |||   || ||  |  ||||    |||   ||  | | |||    | |||   |   |  ||| ||       |  | | |||| ||||| ||||  |  |   ||||||||||| || ||||||||||||||||| || ||||| || || || || || ||||||||||| || ||| || | || || ||  ||| ||| || |
---gtatcctatgcctagcctttggtttctcattgctttattctttcacctttctatatatcttgtcttaaaccaattcgatgctgttatctt-aaccaattgtacacagATGACAAATACCATCCAGAAGAAGTTCAAAGTTTCATCCACGCAGCTTCTGTATCAGTCTTGCCCATATCAAGCAATCACTCTTTTCGTCACTGGGCCAT

upper sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 6
--cctgtaaataag-----cagaagctttttcctcttgc-tgtgtaactctaatgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT
   ||| |  || |     ||  | || |||||||| |    |||   | |  || | |   ||||  || ||||  | |   ||| |||||  |  |  ||    ||||||| || || |||||||||||||||||||| || ||||| |||||||| || || ||||| || || ||| ||||||| |||||  ||  |||||| |
aggctgcatttatgtgtttcaataactatttcctctagggcctgtctttgtgttgtaataatgttta-gtcttgt--ttaagatct-taatcagttcctttt----agATGACGAATACCATCCAGAAGAAGTTCAAGGTTTCTTCAACGCAACTGCTGTATCAATCTTGTCCCTATCAAGCACTGACGCTGTTCATCTCTGGCCCAT

upper sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
lower sequence: EFJ14247 (Selaginella moellendorffii), 3'ss of exon 4
cctgtaaataagcagaagctttttcctcttgctgtgtaactctaatgcatttgagtttctg--ttttgtggtcagtttctgtaatctttaaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT
                                 || |   | | || ||  ||||||| ||  ||||   |    | ||  |||  ||      | | ||||||||| |||||||| ||||| |||||||| || || || || || || || ||||| ||||||||||||||| |    ||  || | || | ||| || |
---------------------------------gtatccttttgattcacctgagtttgtgcgttttccaggggatctccttaacgttcttgtttgcgtcagATGACCAACACTATTCAGAAAAAGTTCAAAGTTTCGTCCACGCAGCTACTATACCAATCTTGCCCTTACCAAGCTACAACGTTGATACTTACTGGTCCTT

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|32788480|gb|CD940716.1|CD940716
EST:     GATCCATACTGTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATT                         ATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTT
genomic: GATCCATACTGTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATTgtatcctttc ... cgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTT
EST: gi|211483724|gb|FL457141.1|FL457141
EST:     GATCCATACTGTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATT                         ATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTT
genomic: GATCCATACTGTCCTTGCTGGCAATTATCACGACTTGCATTGCTCAAATTgtatcctttc ... cgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgttcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT
                                    atctttaac  putative branch site 
                                  taatctttaa  TA-rich tract