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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtagctgggtgctacatcagttccttagttatatctgttggctcagtgataattaatctgatcagtgctttgttatttcctgatgttatggaaatggaagtgagatttcagatgtctattcgctggttttgtagTGTCCTGATCCACACTTCAAAAAGAGACATCACAAAAGAAGAGTTCTGCAGCAACCATTGGTCGATTCAATCATAAATAATCTATGTTTAGGCGGACAG

Basic information

species Zea mays
transcript GRMZM2G054378_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054378_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g35170.1 (Oryza sativa), 3'ss of exon 6
gtgagtgtagctgggtgctacatcagttccttagttatatctgttggctcagtgataattaatctgatcagtgctttgttatttcctgatgttatggaaatggaagtgagatttcagatgtctattcgctggttttgtagTGTCCTGATCCACACTTCAAAAAGAGACATCACAAAAGAAGAGTTCTGCAGCAACCATTGGTCGATTCAATCATAAATAATCTATGTTTAGGCGGACAG
|||||| ||||| ||||  |  ||||||     || |  |  ||||  |  |       || | |  |   || | || | ||   | |||||  ||||   |||        |  ||| | |  |      || | |||||||||||||| || || || ||||| |||||||| ||||||||||| ||    |  ||||| |||||||||| |||||| || |||||||| |||| |
gtgagtatagctaggtgtaatgtcagttttcc-gtgacgttggttgaatatgc------tagtttagttcctggtctgcttttctttcatgtttcggaaccagaa--------tttgatattttct------ttctatagTGTCCTGATCCCCATTTTAAGAAGAGGCATCACAAGAGAAGAGTTCTACAATCGCAGTTGGTGGATTCAATCACAAATAACCTCTGTTTAGGTGGACGG

upper sequence: GRMZM2G054378_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G24260.1 (Glycine max), 3'ss of exon 6
gtgagtgtagctgggtgctacatcagttccttagttatatctgttggctcagtgataattaatctgatcagtgctttgttatttcctgatgttatggaaatggaagtgagatttcagatgtctattcgctggttttgtagTGTCCTGATCCACACTTCAAAAAGAGACATCACAAAAGAAGAGTTCTGCAGCAACCATTGGTCGATTCAATCATAAATAATCTATGTTTAGGCGGACAG
                                ||       ||||| || |   ||  | |  || |  |  | |||   || |  ||   || |     |||      |||||||    ||||| |        || ||||||| || ||||| ||||| || | |||||| |||||||||||||||||| | || ||||| | | | ||  || ||||| ||      || ||||||
---------------------------aggcaagaagggcttgttgactaa--aatgctaatacttaaaaaggttttac-atctaatggccttttttttctggttaaatgatttca---ttctataca-------tgcagTGTCCAGACCCACATTTCAAGAAAAAACATCATAAAAGAAGAGTTCTGCAGAAGCCTTTGGTTGGTGCTATAGTAGATAATTTAATGCCTGGGGGACAG
















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|71430757|gb|DR811807.1|DR811807
EST:     AGAAAATCATATCGTCATACCCTGGTCCCCTGTCACTTGTTTCAATACTG                         TGTCCTGATCCACACTTCAAAAAGAGACATCACAAAAGAAGAGTTCTGCAG
genomic: AGAAAATCATATCGTCATACCCTGGTCCCCTGTCACTTGTTTCAATACTGgtgagtgtag ... ggttttgtagTGTCCTGATCCACACTTCAAAAAGAGACATCACAAAAGAAGAGTTCTGCAG
EST: gi|93017109|gb|EB642629.1|EB642629
EST:     AGAAAATCATATCGTCATACCCTGGTCCCCTGTCACTTGTTTCAATACTG                         TGTCCTGATCCACACTTCAAAAAGAGACATCACAAAAGAAGAGTTCTGCAG
genomic: AGAAAATCATATCGTCATACCCTGGTCCCCTGTCACTTGTTTCAATACTGgtgagtgtag ... ggttttgtagTGTCCTGATCCACACTTCAAAAAGAGACATCACAAAAGAAGAGTTCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatgttatggaaatggaagtgagatttcagatgtctattcgctggttttgtagTGTCCTGATCCACACTTCAAAAAGAGACATCACAAAAGAAGAGTTCTGCAGCAACCATTGGTCGATTCAATCATAAATAATCTATGTTTAGGCGGACAG
 tcctgat  putative branch site (score: 3)
                                               ttttgta  TA-rich tract