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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttagtcataccaaaccaaacggggcctaatatgtcaatatgcagcatgcattcttccaattctggctgtatcatgcaagtggttgacacttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG

Basic information

species Zea mays
transcript GRMZM2G085747_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 4
ctttagtcatacca-aaccaaacggggcctaatatgtcaatatgcagcatgcattcttccaattctggctgtat-catgcaagtggttgacacttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG
  | | |  | | | || | |  |   | | ||    ||  ||   |      |||| |   |  ||    | | |||   | |||  |   ||| ||||||||||||||||||||||||||||||||||| || ||||||||  ||||||| ||||| ||||||||||||||||||||||| |||||||| ||||||||||
-ataaatatttctacaaaccattgaaacttcatgcagcataat-tggttccatttctgcttgtgttgaacctctgcatctgattggccgttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG

upper sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G39870.1 (Glycine max), 3'ss of exon 4
ctttagtcataccaaaccaaacggggcctaatatgtcaatatgcagcatgcattcttccaattctggctg--tatca--tgcaagtggttgaca--cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG
     | | | ||| |    | || || |  |   ||| |  | ||||  | | || |     |||  |   |||    |  || |   |      ||| |||||||| |||||||| ||  |||| ||||| ||||| ||||| ||||| ||||||||||| ||||||||||| || |||||||| || ||||| ||  | ||||
-----gccttgccataattta-ggagctttttggttcagtgagtagcaaacttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG

upper sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G08110.1 (Glycine max), 3'ss of exon 4
-ctttagtcataccaaaccaaacggggcc-taatatgtcaatatgcagcatgcattcttccaattctggctgtatcatgcaagtggttgacactttttt--cagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG
  ||   | |              ||  | | |  || ||| ||   || |||| |  | || |  |   | | |   || |     | |  ||| | |  ||||| |||||||| ||  | || ||||| ||||| ||||| ||||||||||||||||| |||||||| || || || || || || ||||| ||||| ||||
aattccatgactttggtatgttttggttcattaagtgacaaaata-ggcttgcaattgttcattcat---tatgtttggctatcatcttattcttctgttgcagGTAGACATGATTGTCTTAACAGATGGAAGTCGAATTCTTGGCTTAGGTGACCTTGGAGTTCAGGGAATTGGAATCCCCATAGGAAAACTTGATGTGTATG

upper sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G46340.1 (Glycine max), 3'ss of exon 4
ctttagtcataccaaaccaaacggggcctaatatgtcaatatgcagcatgcattcttcc-aattctggctgt-----atcatgcaagtggttgacacttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG
     | | | | | |      || || |  |   ||| |  | ||||  | | || ||    |     | |      | ||   | |   |    ||| |||||||| |||||||| ||  |||| ||||| ||||| ||||| ||||| ||||||||||| ||||||||||| || |||||||| || ||||| ||  | ||| 
----tgccttgctataattt-tggagctttttggttcagtgagtagcaaacttgctccctggcttcatttatttttggttataataatctcttttccttgtttcaGGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTAT-

upper sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G01680.1 (Glycine max), 3'ss of exon 5
-ctttagtcataccaaaccaaacggggcctaatatgtcaatatgcag-catgcattcttccaattctggctgtatcatgcaagtggttgacactttttt--cagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG
  ||   | |              ||   || |  || |  |   || | |||| |  | || |  |   | | |   |  |     | |  ||| | |  ||||| |||||||| ||  | || ||||| ||||| ||||| ||||||||||||||||| |||||||| || || || || || || ||||| ||||| ||||
aattcgatgactttggtatgttttgg-tttattgagtgataaaataggcttgcagttgttcattcat---tatgtttggttatcatcttattcttctgttgcagGTAGACATGATTGTCTTAACAGATGGAAGTCGAATTCTTGGCTTAGGTGACCTTGGAGTTCAGGGAATTGGAATCCCCATAGGAAAACTTGATGTGTATG

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|211274711|gb|FL015918.1|FL015918
EST:     GGATAAGGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCT
genomic: GGATAAGGGGG-AGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCT
EST: gi|74238358|gb|DT646272.1|DT646272
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|149102281|gb|EE287658.2|EE287658
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|211384290|gb|FL369291.1|FL369291
EST:     GATAAGGGGGGAGATGATGTCAATGATTTTACA-CTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGGCTTAGGTGA
genomic: GATAAGGGGG-AGATGATGTCAATGATTT-ACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGG-CTTAGGTGA
EST: gi|33094812|gb|CF054806.1|CF054806
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|32838032|gb|CD977710.1|CD977710
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|32836374|gb|CD976052.1|CD976052
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|211016654|gb|FL375789.1|FL375789
EST:     GATAAGGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAAGA-G                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTGAG-CTTAGGTG
genomic: GATAAGGGGG-AGATGATGTCAATGATTTACAACTGGCCAGCAGA-GAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCT-AGGCTTAGGTG
EST: gi|32801635|gb|CD953871.1|CD953871
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|71437509|gb|DR818559.1|DR818559
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgcattcttccaattctggctgtatcatgcaagtggttgacacttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG
                                     ggttgac  putative branch site (score: 4)
                                           cacttttttc  CT-rich tract
                                            actttttt  TA-rich tract