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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaaataaccatcttgaaaaatatattgttggcaatgtataataacacttgtttttttaatggtttgcaattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG

Basic information

species Zea mays
transcript GRMZM2G113619_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 7
gtaagtgaaataaccatcttgaaaaatat----attgttggc--aatgtataataacacttg----tttttttaatggtttgcaa-ttgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
|| ||||||| ||   |||| ||  || |    ||  |||      |||| |  | || | |    |  | || ||| | |   | |||| |||||||||| |||||||||||||| || ||||| || ||||| || |||||||||||| | |||||||||||||||||||||||| |||||
gtgagtgaaagaatgctctttaactatctggttatcattgttttgttgtacatcatcattagaagttggtattgatgctctattacttgacagCTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG

upper sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 5
gtaagtgaaataa--ccatcttgaaaaa--------tatattgttggcaatgtataataacac-ttgtttttttaa--tggtt-tgcaattgaa------agCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
|| |||||  | |   ||| ||| | ||         | | | || | | || ||   || || ||||     |||  |  ||   |||   ||      |||||||  || | |||||||||||||| ||  | || | ||| ||||||||||||||||||||||| ||||| |||||  |||| ||||| 
gtgagtgactttagttcattttggataagtggttaacacagtatttgtattgcattcaaatacattgtcggcctaacctaattacacaaccaaactctgcagCTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA

upper sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 5
-----------------gtaagtga--aataaccatcttgaaaaatatattgttggcaa-tgtataataacacttgtttttttaatggtttgcaattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
                  | || ||  | |        |   |  | ||||| |  ||| |  || ||    ||    |  | |   |       |    |||||||  || | || ||||||||||| ||  | || | ||| ||||||||||||||||||||||| ||||| |||||  |||| ||||| 
gtgagtgactttagttcattagggataagtggttcatatagtagttgtattgctttcaaatacatcattgggctaacctcatcacatggccattctctgcagCTTTTCTTGCTTCGAGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAA

upper sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 6
------------------gtaagtgaaataaccatcttgaaaaatatattgttggcaatgtataat--aacacttgtttttttaatggtttgcaattg---aaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
                       | |   ||     |  ||   | ||||| |  |||  |  |||  |   |     |  |     | |  | |||      |||||||  || | ||||||||||| || ||  | || | |||||||||||||||||||||||||||  ||||||| ||  |||| ||||| 
gtgagtgatttgagtttttctttttagtcaaattcttccaatgttttattgatttcaaaatgcaatttagagccaacctaatcgtcagctctctattttctgcagCTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA

upper sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G11960.1 (Glycine max), 3'ss of exon 6
-----------------------gtaagtgaaataaccatcttgaaaaatatattgttggc-----aatgtataataacacttgtttttttaatggtttgcaattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
                        | ||| || |      | ||   ||| | || |||       |||| |    |   |     |  |        |    |    |||||||  || | ||||| ||||| || ||  | || | |||||||||||||||||||||||||||  ||||||| ||  |||| ||||| 
gtaagtgatttgagttttttctttttagtcaagttcttcccatgtccaatgttttattgatttcaaaatgcaatgcagagcccacctaatctgctcactattttctgcagCTTTTCTTGCTTCGTGCCGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAA

upper sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
------------------gtaagtgaaataaccatcttgaaaaatatatt---gttggcaatgtataataacacttgtttttttaatggtttgcaattgaa---agCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
                   |   |    |     ||||  |   | | |    ||||    |   |  ||||||          ||| || ||    | |    ||||| | ||| | || |||||||| || || ||||| | ||| |||||||||||||| ||||||||  | |||||||| ||||||||||||
gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaaaccacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG

upper sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtaagtgaa-ataaccatcttgaaaaatatattgttggcaatgtataataacacttgtttttttaatg---gtttgcaattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
                                         ||   || |  |  | ||  |   |  |||||   |||     |  ||      |     ||  |||     |      |||| ||||||| ||| | || |||||||||||||| || || | |||||| ||||| ||||| |||||||| |||||||| || ||||| ||||||
gtgagtgagatatgtgtactattcatttgataataatttgtgtgcttgtatgtgtctatacttgta--tatatccatggttgcatggaagtggtttcaccattaaaatacatatggatgcttgacagCTTTTCCTGCTTCGAGCTGCTGGTTTCCTTCTCCCTTGCTACATTATGGCCTGGGCTATCAGTATATTGCAGCGTCGAAGACAAAGACAG

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:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|19769762|gb|BQ034483.1|BQ034483
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|93283252|gb|EB675516.1|EB675516
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|60337669|gb|DN204642.1|DN204642
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|78086641|gb|DV515034.1|DV515034
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|60338944|gb|DN205917.1|DN205917
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|78106313|gb|DV524731.1|DV524731
EST:     CTGACTCTAACTGATGAAGATGAGGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|19769358|gb|BQ034079.1|BQ034079
EST:     GACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: GACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|71311804|gb|DR792363.1|DR792363
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|91877838|gb|EB407795.1|EB407795
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|71766652|gb|DR964589.1|DR964589
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|78106314|gb|DV524732.1|DV524732
EST:     CTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|76280759|gb|DV020327.1|DV020327
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
EST: gi|211143061|gb|FL281156.1|FL281156
EST:     CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA                         CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT
genomic: CACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCT

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: 48 (upstream exon), 47 (downstream exon)
Score: 141

TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 73

TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 122

TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCAgtaagtgaaa ... caattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgttggcaatgtataataacacttgtttttttaatggtttgcaattgaaagCTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAG
           aatgtataataacact  TA-rich tract