Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttgcacgccatctctgccctcctccttacctcctgatttaagtactcttcatgttcaccggtgcccggcaactgtttcatcctgacgcgtgttgtttccctttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC

Basic information

species Zea mays
transcript GRMZM2G155021_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155021_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g40570.1 (Oryza sativa), 3'ss of exon 1
------------------------gtcttgcacgccatctctgccctcctccttacctcc-tgatttaagt--actcttcatgttcaccggtgcccggcaactgtttcatcctgacgcgtgttgtttccctttgcgc-gcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC
                        | ||  |    |   ||   |    | |||  | || || ||   ||  ||   || || ||  |   ||         ||||  |  ||| |      |   |      ||| ||||||||||| |||| |||||||   |||||||| |||||| |||||||||||||| ||||| | ||||||
gtacggcgccccctgcgcccccaggcctcacctctcccttcactctcgtttcttctcgccatggttgttgttcacctctcgtgctcgacctcgctgacgtgacgtttgttgttgatggcccccgccgctgccgacgccgcagATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTC

upper sequence: GRMZM2G155021_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G49070.1 (Glycine max), 3'ss of exon 1
---------gtcttgcacgccatctctgccctcctccttacctcctgatttaag--tactcttcatgttcaccggtgcccggcaactgtttcatcctgacgcgtgttgtttccctttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC-
            |||      |  |||    |     ||   |   | | ||    |  ||   | | | |   ||    |     || |  |||||     | ||| ||     ||  | | ||||||||||| |||||||||| |||   ||||||||||| || ||||||||| ||| || | ||| ||  
tactctctctaattgtgttgaaattctaaattatgatttttttgggggtgtagaatttttccctacggttaaaagttgatgctttttgatgaatcctttaatgggtttttgtttgtttggtgtagaTCTGCTGTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACCACCTACTCACCGACTGGAGTTG

upper sequence: GRMZM2G155021_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G37570.1 (Glycine max), 3'ss of exon 1
-----------------gtcttgcacgccatctctgccctcctccttacctcctgatttaagtactcttcatgttcaccggtgcccggcaactgtttcatcctgacgcgtgttgtttccctttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC
                  | ||| |   |   |      |  |  ||       | |  || |  || | |   | |    |    |     || |  ||||| |   | ||| ||     ||  | | ||||||||||| |||||||||| |||   ||||||||||| || ||||||||| ||| |||| ||| || 
gtactctctctctaattatgttgaaattctattaaattgtggttttt-ttggggggtagaatttttccttactgttaaaaattggtgctttttgatgaatcctaa-atgggtttttgtttgtttggtgtagATCTGCTGTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACCACCTACTCACCCACTGGAGTT

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|211256321|gb|FL030999.1|FL030999
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|76287240|gb|DV026808.1|DV026808
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|211331694|gb|FL020929.1|FL020929
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|22521527|gb|BU080338.1|BU080338
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|71432321|gb|DR813371.1|DR813371
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|211331700|gb|FL020935.1|FL020935
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|33102963|gb|CF062923.1|CF062923
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|71425209|gb|DR806571.1|DR806571
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|211331696|gb|FL020931.1|FL020931
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|67041269|gb|CO467524.1|CO467524
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|21987817|gb|BQ779345.1|BQ779345
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|20512879|gb|BQ280071.1|BQ280071
EST:     ACCACCATGGCGCGCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: ACCACCATGGCAC-CCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|211331704|gb|FL020939.1|FL020939
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|33102108|gb|CF062068.1|CF062068
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|101397701|gb|EB820731.1|EB820731
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|88752281|gb|DY536422.1|DY536422
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|22472298|gb|BU036778.1|BU036778
EST:     CACCACCATGGCACCCGG-CTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|74244464|gb|DT652378.1|DT652378
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|211331699|gb|FL020934.1|FL020934
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|211331695|gb|FL020930.1|FL020930
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|37423435|gb|CF649445.1|CF649445
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|91874353|gb|EB404310.1|EB404310
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|67020552|gb|CO449301.1|CO449301
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|78112263|gb|DV530657.1|DV530657
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|211331701|gb|FL020936.1|FL020936
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|211331703|gb|FL020938.1|FL020938
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|37425454|gb|CF650468.1|CF650468
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTGACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT
EST: gi|32907826|gb|CF012639.1|CF012639
EST:     CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAG                         ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTGCCTCACCACCT
genomic: CACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCT

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), 46 (downstream exon)
Score: 38

CTCCCTCCTCTGTCCTCCGTACCACTCGTCTTCGTCTAGCCGCCGACCGCCACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 59

CTCCCTCCTCTGTCCTCCGTACCACTCGTCTTCGTCTAGCCGCCGACCGCCACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

CTCCCTCCTCTGTCCTCCGTACCACTCGTCTTCGTCTAGCCGCCGACCGCCACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 52

CTCCCTCCTCTGTCCTCCGTACCACTCGTCTTCGTCTAGCCGCCGACCGCCACCACCATGGCACCCGGCCTCTACACCGACATCGGCAAGAAGACCAGAGgtcttgcacg ... ttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accggtgcccggcaactgtttcatcctgacgcgtgttgtttccctttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC
                       tcctgac  putative branch site (score: 52)
                                 tgttgtttcccttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttgcacgccatctctgccctcctccttacctcctgatttaagtactcttcatgttcaccggtgcccggcaactgtttcatcctgacgcgtgttgtttccctttgcgcgcagATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT