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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgttgacatgtgatcaatttattcatcctggattattagttcatgctgataacaggagtgataatgtttgataccaagcacatct...

Basic information

species Zea mays
transcript GRMZM2G106213_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 2
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgt--tgacatgtgatcaatttattcatcctggattattagttcatgctgataacaggagtgataatgtttgataccaagcacatct
||||||||||||||||||||||||||  || |||||||| ||||| || ||||| || ||||| || || ||||| ||||||||||| ||||||||||||||||||| ||| ||||||  | || ||  |    |||  |  |  |    ||||||||     |||       |||| |||| |||| ||| | |||  |  
CTCGAGGGCCTATGGAAACAACATTGGTGGTTACAAGAACGAGGGGTTTGTTGAAGTTCTTGCTGCGCAGCAGAGCCCAGAGAATCCTAACTGGTTTCAGgtatcttggttaatctgtattaacttgccaaattttttatagtagtactgtattagtttgaattgactcggtaagtggtaatttttg-tactatgcaggta-

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 2
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgttgacatgtgatcaatttattcatcctggattattagttcatgctgataacaggagtgataatgtttgataccaagcacatct-------
 ||  | || |||| || |||||| |  || ||||| ||||||||||| |||||||| ||||| || || |||||||| |||||||| || ||||| ||||||          |   |||        | |||||    | |  |   |  |   |  |  ||      |   | ||  | |   | ||   |              
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgaccacattgccttgtttgactctaaattttgatacctcgcgatgatgacttttcttgtcccttgattttattttttaacaaacttggtgtgatcattgcag

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgttgacatgtgatcaatttattcatcctggattattagttcatgctgataacaggagtgataatgtttgataccaagcacatct-------
 ||  | || |||| || |||||| |  || ||||| ||||||||||| |||||||| ||||| || || |||||||| |||||||| || ||||| ||||||          |   |||||      | |||||    | | ||   |  ||  |  || ||      |   ||||  | |   | ||   |              
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactc----taaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 2
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgttgacatgtgatcaatttattcatcctggattattagttcatgctgat-aacaggagtgataatgtttgataccaagcacatct
 ||  |||| ||||  |  ||||| |  |||||||||||||| || || ||||| || ||||| || || |||||||| ||||| ||||||||||||||||||      |    ||   |   |||| |      | ||||  |     |||  | ||  ||  | ||    | || |  ||||||||  |||  |   | 
TTCCCGGGCTTATGCCAGTAACATGGGTGGGTACAAGAATGAAGGGTTTGTTGAAGTTCTTGCTGCTCAGCAGAGTCCTGAGAACCCCAACTGGTTTCAGgtaagaacatcgtgcttcagtggtgtgcttggaa-actcattttttggaattcctgcaatctcttcaattctattgtttctgtttgatttcaaaaattcca

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 5'ss of exon 2
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgttgacatgtgatcaatttattcatcctggattattagttcatgctgataacaggagtgataatgtttgataccaagcacatct----
 ||  | || || |  |  ||||| |  |||||||||||||| || ||||| |||||  | || || || |||||||| |||||||| || |||||||||||||  |    |   | |  |      |||      ||     |||  | |    |  | |||| ||         |  |   ||||  |   |||        
GTCCCGAGCTTACGCTAGTAACATGGGAGGGTACAAGAATGAAGGTTTCGTGGAGGTTTTGGCTGCCCAGCAGAGTCCCGAGAATCCTAATTGGTTTCAGgtatgat-acctgcatat-aattcacaatcgtgggtttttgaatgggctgtgcaattct-ctgagaatcttcccagtcttacctgatgtcct-cacgctgagat

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S239_45V6.1 (Physcomitrella patens), 5'ss of exon 2
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttat--ctgttgacatgtgatcaatttattcatcctggattattagttcatgctga--taacaggagtgataatgtttgataccaagcacatct
 ||  | || || |  |  ||||| |  ||||||||||| ||||| ||||| || ||| | || || |||||||| || || || ||||||||||||||||| |  |   | ||  || || | |  |  |  ||||  ||    | | | |||  | |  ||     | |||  |      |  | |||| |   ||||    
GTCCCGAGCATACGCTAGTAACATGGGAGGGTACAAGAACGAGGGCTTCGTGGAAGTCTTGGCTGCTCAACAGAGCCCCGAAAACCCCAACTGGTTTCAGgtgttgtacctgattcctcttcaaagttcgtggattttctctatgtagttcattt-tacgcgccagatttacaccacgttctacttctgat-ctgcgcacga--

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ17026 (Selaginella moellendorffii), 5'ss of exon 2
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgttgacatgtgatcaatttattcatcctggattattagttcatgctgataacaggagtgataatgtttgataccaagcacatct
 ||| | || |||   |  ||||| |     |||||||| || |||||||| ||||| || || || ||||| ||||| |||||||| |||||||||||||||  | |  | |   |||   | ||  ||    | | || |    ||| ||  ||   |                                        
ATCGCGAGCTTATTCCAGTAACATGGGAAACTACAAGAACGAAGGATTCGTGGAGGTTCTCGCTGCTCAACAAAGTCCCGAGAATCCTAACTGGTTTCAGgtaattgttctcaaa-gtttttaagttctcgcagt-tccagctgaaattgttttttgtag----------------------------------------

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ16157 (Selaginella moellendorffii), 5'ss of exon 2
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgttgacatgtgatcaatttattcatcctggattattagttcatgctgataacaggagtgataatgtttgataccaagcacatct
 ||| | || |||   |  ||||| |     |||||||| || |||||||| ||||| || || || ||||| ||||| |||||||| |||||||||||||||  | |  | |   |||   | ||  ||    | | || |      | ||  |  |                                          
ATCGCGAGCTTATTCCAGTAACATGGGAAACTACAAGAACGAAGGATTCGTGGAGGTTCTCGCTGCTCAACAAAGTCCCGAGAATCCTAACTGGTTTCAGgtaattgttctcaaa-gtttttaagttctcgcagt-tccagctgaagctgtttttgtag-----------------------------------------

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|31354893|gb|CD439250.1|CD439250
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|148987334|gb|EE031175.2|EE031175
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|60355358|gb|DN222331.1|DN222331
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCACAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|67027741|gb|CO456490.1|CO456490
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATGTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|71303914|gb|DR788076.1|DR788076
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|148966536|gb|EE017559.2|EE017559
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCCACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|148950461|gb|EC896031.2|EC896031
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|154130546|gb|EC872338.2|EC872338
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|31356252|gb|CD440609.1|CD440609
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|211191066|gb|FL114963.1|FL114963
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCG
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCG
EST: gi|148967973|gb|EE019294.2|EE019294
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
EST: gi|6564057|gb|AW231679.1|AW231679
EST:     TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAG                         GGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT
genomic: TTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAAT

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: 336

CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 10

CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 126

CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgt ... ccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT