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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctcgagcactatgtttccagagcaccttttatcatatttcaagttttgtatgtctttcaagtaatgttttcctaaccattatgtacctctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATT

Basic information

species Zea mays
transcript GRMZM2G047855_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 3'ss of exon 1
ttctcgagc--actatgtttccagagcaccttttatcatatttcaagttttgtatgtctttcaagtaatgttttcctaaccattatg-tacctctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATT
|| || |    | | |  || |       | || |      |   ||  |  |||| ||| ||   |||   |  ||||| |||||| | | ||||| || ||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||  |||||||||||||||| 
ttgtccatttaattcttgttacctcaagtcattgagggacctggcagcatgttatgacttaca--caatacctcgctaactattatggtgcatctttaac-agTGAGCAGGATGACTATGAAGTTGTCAGGAAAGTTGGAAGAGGTAAATATAGTGAAGTCTTTGAAGGCATCAATGTTAACAACAATGAGAAATGCATCATC
















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|67025945|gb|CO454694.1|CO454694
EST:     CACCGTCCTATCGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|67040594|gb|CO466849.1|CO466849
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|60357494|gb|DN224467.1|DN224467
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|94472121|gb|EB701079.1|EB701079
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|149072965|gb|EE161226.2|EE161226
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|32870874|gb|CF010556.1|CF010556
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|211275426|gb|FK954599.1|FK954599
EST:     CTGCGTCCCAASGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|148932884|gb|EE285654.2|EE285654
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|149039473|gb|EE046613.2|EE046613
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|149109955|gb|EE293764.2|EE293764
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGATAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|87156044|gb|DY400833.1|DY400833
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|31911129|gb|CD651772.1|CD651772
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|149104221|gb|EE289654.2|EE289654
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|149072883|gb|EE161139.2|EE161139
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|26559480|gb|CA831715.1|CA831715
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGT
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGT
EST: gi|60353455|gb|DN220428.1|DN220428
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|211273620|gb|FK954594.1|FK954594
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|149097607|gb|EE183500.2|EE183500
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|211275425|gb|FK954598.1|FK954598
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|211275428|gb|FK954601.1|FK954601
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCACGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|211273622|gb|FK954596.1|FK954596
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|30031785|gb|CB833636.1|CB833636
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|148971083|gb|EE021924.2|EE021924
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|31997699|gb|CD661721.1|CD661721
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|30705447|gb|CD058786.1|CD058786
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|71446427|gb|DR827477.1|DR827477
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|211273621|gb|FK954595.1|FK954595
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
EST: gi|71441899|gb|DR822949.1|DR822949
EST:     CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGG                         TGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG
genomic: CTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAG

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), 48 (downstream exon)
Score: 169

GATCCGGGCCCCTCATGTCGAAGGCAAAGGTCTACACCGACGTCAACGTTCTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 243

GATCCGGGCCCCTCATGTCGAAGGCAAAGGTCTACACCGACGTCAACGTTCTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 396

GATCCGGGCCCCTCATGTCGAAGGCAAAGGTCTACACCGACGTCAACGTTCTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

GATCCGGGCCCCTCATGTCGAAGGCAAAGGTCTACACCGACGTCAACGTTCTGCGTCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTCCAATGGGGgtaagtgatt ... ctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtatgtctttcaagtaatgttttcctaaccattatgtacctctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATT
                          tcctaac  putative branch site (score: 188)
                                        tacctcttt  putative PPT
                  taatgtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctcgagcactatgtttccagagcaccttttatcatatttcaagttttgtatgtctttcaagtaatgttttcctaaccattatgtacctctttgaccagTGAGCAGGATGACTATGAAGTTGTCAGAAAAGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - atgtttc
- - - - - - - - - - -gagcacc
- - - - - - - - - - - - - - - - - - - - - - - -ttgtatg