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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG

Basic information

species Zea mays
transcript GRMZM2G169914_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g19460.1 (Oryza sativa), 3'ss of exon 2
---agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgc-ttgacgtgccttttacaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
    |   | | ||  ||   | || ||| |  |    || |   || ||     | || || | | ||  | | |     | |  |  | ||| ||||| ||||||| |   | |||||||| ||||| |||||||||||||| |||||| | |||||||||||||||||||| ||||||||||||
tcagggaatgtgtaaacattggatg-attcaattagcaggaacgaaaagtta---tagtagtacatctggtttagtcaagcttatatagccttttcaatttcagAGGGTGTAATAGCTGGAGGTGCTGCCGGTGTTGTTGTTGAGACAGCTCTGTATCCTATTGATACAATAAAAACCAGGCTTCAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G36580.3 (Glycine max), 3'ss of exon 3
----agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
    | |  |  |   | | ||  |   | ||   || |  | ||| ||  |    | |||||        || ||  | |     |   |  |  |||| |||| ||   | | |||||||| ||||||||||||||||| |||||||||||||| || |||||||| || || ||  | || |||
ggctataagttgcatcttatcacatatgtcta---ttgtcttgtactattaatatattgttgtgggacatacttatgagttatgaatat-tgatctaattgcagATGGTTGCATTGCTGGAGGTGCTGCTGGTGTTGTTGTAGAAACAGCTTTATACCCCATTGATACCATCAAAACTCGACTACAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G15150.1 (Glycine max), 3'ss of exon 2
-agagttctctattcagcagttggatttagatttatggtatacaatgtaggct-tggttgtccttatgcctca-tttgcttgacgtgccttttacaattc-cagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
 | |||  | |||      | |   || |    ||    |||| || ||     ||| | |  |||    ||| |||   ||| | ||    |  ||||  ||||||| |   | || || ||  | ||||| ||||||||||||||||||||||| || ||||| |||||||| ||  | || |||
aatagtattttatcttcttgctaagttca----tagacaatactatatacttgatggattttattacatttcaatttttctgatgagctagatggaatttgcagAGGGCGTTATTGCAGGTGGTACAGCTGGAGTTGTTGTTGAAACAGCTTTATACCCAATTGACACAATAAAAACACGTCTGCAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G31870.1 (Glycine max), 3'ss of exon 3
agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttg--tccttatgcctca-tttgcttgacgtgccttttacaattc-cagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
  | |  | | || | |  || |   ||  ||  |     | | | ||  |||| | |  |  |||    ||| | |   ||| | ||    |  ||||  ||||||| |   | || |||||  | ||||| ||||||||||||||||||||||| || || || |||||||| ||  | || |||
-aaatagtat-tttacctttttg--ctaagttggtaaacaatactatatacttgatgggtttattacatttcaatctttctgatgagctagatgaaatttgcagAGGGCGTTATTGCAGGAGGTACAGCTGGAGTTGTTGTTGAAACAGCTTTATACCCAATCGACACAATAAAAACACGTCTGCAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G39460.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------------------------------agagttctctattca--gcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaat--tccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG----
                                                                                             | |||| | || |  ||   | | ||   |||| || | |  |  |   ||||    ||   || | ||  ||    | | ||     ||   ||  | ||||||||    | || |||||  | ||||| ||||| ||||||||||||||||| || |||||||| || ||||| || ||||||    
gtttgtgtatattttgtcttttggttcatttgcaactattattttatgaatctcatgttctgactcatatacagtccttgtatctgaaaagtaatttctttttttattgctaatagtttggcatttttgctttgaatcggcagcttcag-gtgtctaagtcttgttattcttatgttttggttttgatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0157g00180.t01 (Vitis vinifera), 3'ss of exon 2
agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttgtcctta-tgcctcatttgcttgacgtgccttt-tacaattccagAGGGGGCCTTG--GCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
    || | ||||      ||   |    | ||      ||  |   |  |  |    | |||| |  || ||     | | ||    || |    ||    || ||| ||||  ||||||||   ||||||||||||||||||| ||||||||||||| |||||||||||||| || || ||||||
----ttttttatttttattttctttgccaaatttcatcttatgacaaaatcacgtccttgcttaatatcttatgcttctaatgttttgttatgggtttttgcagAGGGTCTTGTAGCTGGAGGTATTGCTGGTGTTGTTGTTGAAGCAGCTTTATATCCAATTGATACAATAAAAACTAGACTTCAG

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|211410757|gb|FL164832.1|FL164832
EST:     GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTG                         AGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
genomic: GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
EST: gi|211312002|gb|FL324783.1|FL324783
EST:     GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTG                         AGGGGGSSTTNGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
genomic: GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
EST: gi|88752899|gb|DY537040.1|DY537040
EST:     GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTG                         AGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
genomic: GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
                             gcttgac  putative branch site (score: 4)
                                       ccttttac  putative PPT
                                         ttttacaatt  TA-rich tract