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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_T05
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|71437509|gb|DR818559.1|DR818559
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|32838032|gb|CD977710.1|CD977710
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|32836374|gb|CD976052.1|CD976052
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
EST: gi|32801635|gb|CD953871.1|CD953871
EST:     AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAG                         GTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC
genomic: AGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 190

AAATTACAGCGGTCTGTTCAGACGACCCCGTGGGATGTATTTCAGTGCAAAGGATAAGGGGGAGATGATGTCAATGATTTACAACTGGCCAGCAGAGAAGgtatagctga ... cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgcattcttccaattctggctgtatcatgcaagtggttgacacttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG
                                     ggttgac  putative branch site (score: 190)
                                           cacttttttc  CT-rich tract
                                            actttttt  TA-rich tract