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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttctttgcctcatacacaaatctgaatatgcagcacattcttgcataccttttctaatactctgagtaagatgtggtcgatgctacatatttcttt...

Basic information

species Zea mays
transcript GRMZM2G036534_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036534_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 5'ss of exon 3
CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttctttgcctcatacacaaatctgaatatgcagcacattcttgcataccttttctaatactctgagtaagatgtggtcgatgctacatatttcttt--
|| ||||||||||| ||||| ||||||||||||||||| || |||||||| ||||| |||||||| ||||||||||| ||||| ||||||| ||  ||    | ||||||||  | ||| || ||| ||||  |    |  |||    ||| | |   | |||||      | |   ||  | |  ||  
CTCGACATTTATTCTTTGTCGAGGAAATGGAAGGAGTTAGTCGATAAGGCTCGAGCGAAGCAGCTACAGCCCCATGAATACAATTCTGgtactttctttgtccgtacacaaaattaaatgtgtagctcattgatattcaattttctatatattatc--tgagatggttataaggaatcaactgttcttgg

upper sequence: GRMZM2G036534_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G35960.1 (Glycine max), 5'ss of exon 4
CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatt-tctttgc---ctcatacacaaatctgaatatgcagcacattcttgcataccttttctaatactctgagtaagatgtggtcgatgctacatatttcttt
 ||||  | |||||||||||||| || ||||||||||||||||| |||||  |||| |||||||| || || ||||| |||||| |||||||  |  || |   ||  ||    | |  |  | ||  | | |||  || ||   ||||| |||  |   | | |    |     ||  ||  ||       
ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaattacatacttgtattttattgggtttctgttgtatattaatgaatgaattttccaat-ttaaaattgaatccttaaaaattgtaggtaggca---

upper sequence: GRMZM2G036534_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G31630.1 (Glycine max), 5'ss of exon 4
CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttct-ttgc---ctcatacacaaatctgaatatgcagcacattcttgcataccttttctaat---actctgagtaagatgtggtcgatgctacatatttcttt
 ||||  | |||||||||||||| || |||||||||||||||||||||||  |||| |||||||| || || ||||| |||||| ||||||   |  || |   ||  ||    | |  |  | |   | | |||  || ||   ||||| |||   |   ||| |         | | ||  |   |       
ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaattacatacttgtattttattgggtttcttttgtatattaatgaatggattttccaatttaaaattgaatccttaaaaattgttggcaggca-------

upper sequence: GRMZM2G036534_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G34430.1 (Arabidopsis thaliana), 5'ss of exon 3
CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttctttgcctcatacacaaatctgaat--atgcagcacattcttgcataccttttctaatactctgagtaagatgtggtcgatgctacatatttcttt
 ||||||||||||| || || || |||||||| || |||||||||||||| ||||| |||||||||||||| || ||||||||| |||||| | ||    ||   | |   |  ||| |  |    |   | || | ||      || |   | |||   |    |    ||  | |    || ||    
GTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTGgtaatcctactactagaatattgaagtgatttgagtttgagtaatccttcaactagattgtttgagtcttgttgtttttatttcccttccgggtaattgcag

upper sequence: GRMZM2G036534_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 5'ss of exon 3
CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatt-tctttgcctcatacacaa--atctgaatatgcagcacattcttgcataccttttctaatactctgagtaagatgtggtcgatgctacatatttcttt
 | |||||||||||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||| || ||||| |||||  | |||||  || || | || ||||||   ||   |  || ||  |  ||      | |  |   | ||        |   || |  | |||  || |||       
GTGGACATTTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCCGAGCAAAGCAGCTGCAACCTCATGAATACAATACAGgtatcctcattacatcctacacactcattacatcatacaagatgtttccttgtgcaataattgatggctcatatct-atatattagata-tagatagacacc-

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|6539042|gb|AW225181.1|AW225181
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|6865176|gb|AW360526.1|AW360526
EST:     TTGATAAGGCGCGAGCANNAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: TTGATAAGGCGCGAGCA--AAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|78106198|gb|DV524616.1|DV524616
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|23357491|gb|BU645140.1|BU645140
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|24768304|gb|CA403433.1|CA403433
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|211440164|gb|FL434174.1|FL434174
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|6022391|gb|AW067319.1|AW067319
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|71765103|gb|DR963040.1|DR963040
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|60344293|gb|DN211266.1|DN211266
EST:     GCCCCATGAGTACAACTTTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|78088435|gb|DV516828.1|DV516828
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|149027250|gb|EE046447.2|EE046447
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAATTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|93013412|gb|EB638932.1|EB638932
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|71444183|gb|DR825233.1|DR825233
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|93284411|gb|EB676675.1|EB676675
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|83279414|gb|DV943422.1|DV943422
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|74246257|gb|DT654171.1|DT654171
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAATTTTG                         GCACCTTTACTCTTTTGAATCTTGGTATGTTTGGAGTTGATAGGTTGGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|78074314|gb|DV502748.1|DV502748
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|71759734|gb|DR957671.1|DR957671
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|74236968|gb|DT644882.1|DT644882
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
EST: gi|149035803|gb|EE155127.2|EE155127
EST:     GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG                         GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG
genomic: GGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATG

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: 138

CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 110

CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttcttt ... cattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatttctttgcctcatacacaaatctgaatatgcagcacattcttgcataccttttctaatactctgagtaagatgtggtcgatgctacatatttcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG