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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_T03
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|76280759|gb|DV020327.1|DV020327
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|37399815|gb|CF637245.1|CF637245
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|19769762|gb|BQ034483.1|BQ034483
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|6827480|gb|AW331123.1|AW331123
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|60338944|gb|DN205917.1|DN205917
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|50325342|gb|CO520468.1|CO520468
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTTTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|86471507|gb|DY237877.1|DY237877
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|78106313|gb|DV524731.1|DV524731
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|93283252|gb|EB675516.1|EB675516
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGAC--AG--A-                         GA--CAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|19769358|gb|BQ034079.1|BQ034079
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|71311804|gb|DR792363.1|DR792363
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|91877838|gb|EB407795.1|EB407795
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|211143061|gb|FL281156.1|FL281156
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|60337669|gb|DN204642.1|DN204642
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|19822097|gb|BQ048121.1|BQ048121
EST:     ACATCATGGCGTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
EST: gi|78106314|gb|DV524732.1|DV524732
EST:     ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG                         GAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC
genomic: ACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGC

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 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 17 (downstream exon)
Score: 1

CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaat ... gtctgtccagGAGGCAGCTGCTCTAGCTGCAGCGGAGGTGGCATTCATCCTGCAGTCAGGCCAAGGAAGGGGAGTGCATTTCACCATCGCACCGGACTCCCCGGCCACAC




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