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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttccttttcttattttttgaaggttccgggaacacctaacgtatttcttgccatacaccgaatac...

Basic information

species Zea mays
transcript GRMZM2G113619_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttccttttcttattttttgaaggttccgggaacacctaacg-tatttcttgccatacaccgaatac
|||||||| |||||||||||||| || ||||| || ||||| || |||||||||||| | |||||||||||||||||||||||| |||||||||||   | ||     | |||| |      || |||   |  ||    ||||   |  |  ||||    | |   | ||  |||  ||   ||   | |
CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgttatcatacaggtgatttacattattttctactattttaaatttgttagaacttggaatgtgtgataattttatttgttat-tgccttgttc

upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttccttttcttattttttga---aggttccggga---acacctaacgtatttcttgccatacaccgaatac
|||||  || | ||||||||||| || ||  | || | |||||||||||||||||||||||||||  ||||||| ||  |||| ||||| ||||||   |||||       | ||||||| ||  ||   || | | | ||| |    | ||| | | |   |  |  |  | |    |     || || |     
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtct-taattatagttatcaatattttcagttttgcttgcatgtgtttggtttcacgttacagaattgattctgagtgcagaattgattttagacag-----

upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G04870.1 (Glycine max), 5'ss of exon 6
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagtt--aataatttctaaagtgaatatttgcatcttccttttcttattttttgaaggttccgggaacacctaacgtatttcttgccatacaccgaatac-
|||||  || | |||||||||||||| ||  | || | ||| ||||||||||||||||||||||| ||||| |||||  |||| ||||| || ||||  | |  |   |      ||| ||||  ||   |||| || |||   ||  ||||  |        | |  | || |||      | || | |   
CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAAgtaagtttcagtcttggttctgactaatttttgt-tccgactttgctaattcggtgttggttt-gttctgttttgaaatcttgctttttg-gctccaactttg

upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G11960.1 (Glycine max), 5'ss of exon 7
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttccttttcttattttttgaa--ggttccggga-----acacctaacgtatttctt----gccatacaccgaatac----------------------------------------
|||||  || | ||||| ||||| || ||  | || | |||||||||||||||||||||||||||  ||||||| ||  |||| ||||| ||||||   | |||       | ||||||||  | |   ||| |||| |   || |    || ||| |     | || | | |  ||  ||    ||   |  |  ||                                           
CTTTTCTTGCTTCGTGCCGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtct-tcattatagttattaatatttgt-tttggttttgcttagtcagtgtatcattttcggaataaaaatactttatggtttctttttaggctgcaatctaaaagtttgtgatcatatctcacatttttgtgttatggtgaaacag

upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G35750.2 (Glycine max), 5'ss of exon 6
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttc-cttttcttattttttgaaggttccgggaacacctaa--cgtatttcttgccatacaccgaatac
|||||  || | || ||||||||||| ||  | || | ||| ||||||||||||||||||||||| ||||| |||||  |||| ||||| || ||||   | | |      ||| || ||  ||  |   |||||| |||   ||  ||||            ||  | |  |||||| |    ||    |  
CTTTTCTTGCTTCGAGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAAgtaagttt-cagtcttggttctgactaattttattctgatttttctaattcggtgttggtttgttctgttttgaaatcatgcttcttggctccaactttgt--

upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 5'ss of exon 7
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagt----taataatttctaaagtgaatattt------gcatcttccttttcttattttttgaaggttccgggaacacctaacgtattt-cttgccatacaccgaatac----
||| | ||| | || |||||||| || || ||||| | ||| |||||||||||||| ||||||||  | |||||||| |||||||||||||| |||    ||| || |  |  |  || | ||       |  | ||  |||||||| | ||| | |  ||         |    ||||   |||    ||  |||| |      
CTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgttagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactgttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT2G02960.5 (Arabidopsis thaliana), 5'ss of exon 5
----------CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagt----taataatttctaaagtgaatattt------gcatcttccttttcttattttttgaaggttccgggaacacctaacgtattt-cttgccatacaccgaatac----
          ||| | ||| | || |||||||| || || ||||| | ||| |||||||||||||| ||||||||  | |||||||| |||||||||||||| |||    ||| || |  |  |  || | ||       |  | ||  |||||||| | ||| | |  ||         |    ||||   |||    ||  |||| |      
CTTATTTTAGCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgttagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactgttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 7
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttccttttcttattttttgaaggt----tccgggaacacctaacgtatttcttgccatacaccgaatac--
||||| ||| | || |||||||||||||| || || | |||||| ||||| ||||| |||||||| |||||||| || ||||| |||||||| |||   |   ||      || || |||| ||           |        ||  |    |||   |  |||||  ||   | |  | | | |   ||| |  
CTTTTCCTGCTTCGAGCTGCTGGTTTCCTTCTCCCTTGCTACATTATGGCCTGGGCTATCAGTATATTGCAGCGTCGAAGACAAAGACAGgttagtgtttggctt------tgcatttttgtatagaataaaatatgaagagaaaaaatattctccttcaggacctatggtgggtatgccaaaagaaaaaatgcag

upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 9
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagt----taataattt----ctaaagtgaatatttgcatcttccttttcttattttttgaaggttccgggaacacctaacgtatttcttgccatacaccgaatac
|||||  || | || |||||||| ||  | || || | |||||| ||||| ||||| || |||||||||||||| || |||||||| ||||| |||      ||| |||     |||    |||  ||  |  ||||  |    || | ||     | |       | ||  | | | |||| |  |  ||       
CTTTTCTTGCTTCGGGCTGCTGGGTTTTTACTGCCCTGCTACATTATGGCCTGGGCCATTAGTATCTTGCAGCGTCGAAGACAGAGGCAGgttagtgtctccatattttgtggttaaccataattcttatacattcccatcaacatgtcttttct-tccttttcctatctgccctttctcttcctttgtac-------

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|6827480|gb|AW331123.1|AW331123
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|19769762|gb|BQ034483.1|BQ034483
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|93283252|gb|EB675516.1|EB675516
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         CTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAA
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcagCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAA
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|60337669|gb|DN204642.1|DN204642
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|78086641|gb|DV515034.1|DV515034
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         G
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcag-
EST: gi|60338944|gb|DN205917.1|DN205917
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|78106313|gb|DV524731.1|DV524731
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|19769358|gb|BQ034079.1|BQ034079
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|71311804|gb|DR792363.1|DR792363
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|91877838|gb|EB407795.1|EB407795
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|71766652|gb|DR964589.1|DR964589
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|78106314|gb|DV524732.1|DV524732
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|76280759|gb|DV020327.1|DV020327
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg
EST: gi|211143061|gb|FL281156.1|FL281156
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGGAGGCAG                   
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-GA--CAGgtcagttaat ... cagg

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: 47 (upstream exon), 49 (downstream exon)
Score: 48

CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcagCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACACCACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcagCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACACCACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcagCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACACCACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... caggaggcagCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACACCACAGCA