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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCGGTTCTGTTGGTGCCACCATCCGTGTCTACATCGAGCAATACGAGAAGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataatttccccgtccttttgatttacagagctgaatatactaggggtgaagaaacatttggatcatcatccattaccacctctaagaatcagatt...

Basic information

species Zea mays
transcript GRMZM2G023289_T03
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 17
AACCGGTTCTGTTGGTGCCACCATCCGTGTCTACATCGAGCAATACGAGAAGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataatttccccgtccttttgatttacagagctgaatatactaggggtgaa-----gaaacatttggatcatcatcca--ttaccacctctaagaatcagatt-------
||| || ||||||||||| || |||||||||||||||||||| || ||||||||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||| |    | | ||   || | ||| |      ||   |  |  | |  |      | | | |||   |||   |  |  | | ||  ||| |  ||| | ||       
AACTGGCTCTGTTGGTGCTACTATCCGTGTCTACATCGAGCAGTATGAGAAGGATTCTTCCAAGACCGGCAGGGATTCGCAGGATGCCCTTGCTCCTCTGgtaagacatccgcgctgtatattggctttgccttttggaccgttttccgagcaagtttgcggacctttttcttcagactttaattcagcaaatctgaccatctgctttatccag

upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 17
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 18
AACCGGTTCTGTTGGTGCCACCATCCGTGTCTACATCGAGCAATACGAGAAGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataatttccccgtccttttgatttacagagctgaatatactaggggtgaagaaacatttggatcatcatccattaccacctctaagaatcagatt
||| || || |  ||||| |||||||||||||| || ||||| || ||||||||||| || ||||| || |||||||| || || ||||||| ||| || || ||| |   || |  ||  ||| ||    |  | | |  |  ||     |||  | |  ||| |     | |            | |           
AACTGGCTCAGAAGGTGCAACCATCCGTGTCTATATTGAGCAGTATGAGAAGGATTCGTCAAAGACTGGGAGGGATTCTCAAGAAGCCCTTGGTCCTCTTgtgagaca---tctctctctcttttatcaggactgtttatcaccctgcttttgatcatatcttttggctgacctatgcatttgatcccag----------
















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|78108858|gb|DV527275.1|DV527275
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|71426274|gb|DR807324.1|DR807324
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|5296174|gb|AI782854.1|AI782854
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|211541121|gb|FL006422.1|FL006422
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|113799947|gb|DW921163.1|DW921163
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAG
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAG
EST: gi|32906153|gb|CF010966.1|CF010966
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|5895776|gb|AW037022.1|AW037022
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|78024768|gb|DV493155.1|DV493155
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|31357336|gb|CD441693.1|CD441693
EST:     AGGAAACATCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|67020139|gb|CO448888.1|CO448888
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|32850278|gb|CD989959.1|CD989959
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGT
EST: gi|211190026|gb|FL186116.1|FL186116
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|149060808|gb|EE157260.2|EE157260
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|5081034|gb|AI738296.1|AI738296
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|78109659|gb|DV528075.1|DV528075
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
EST: gi|44900765|gb|CK827310.1|CK827310
EST:     AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTG                         GTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT
genomic: AGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCT

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), 49 (downstream exon)
Score: 347

AACCGGTTCTGTTGGTGCCACCATCCGTGTCTACATCGAGCAATACGAGAAGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGAGTGATTTACAATGAGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 303

AACCGGTTCTGTTGGTGCCACCATCCGTGTCTACATCGAGCAATACGAGAAGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGAGTGATTTACAATGAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 346

AACCGGTTCTGTTGGTGCCACCATCCGTGTCTACATCGAGCAATACGAGAAGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGAGTGATTTACAATGAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 516

AACCGGTTCTGTTGGTGCCACCATCCGTGTCTACATCGAGCAATACGAGAAGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataat ... ttcatctcagGTTGATGTTGCGCTCAAGCTCTCCAAGATGCAAGAGTACACTGGCCGCTCTGCCCCCACCGTTATCACATAAATTTTTGAAGAGTGATTTACAATGAGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCGGTTCTGTTGGTGCCACCATCCGTGTCTACATCGAGCAATACGAGAAGGATTCCTCCAAGACCGGCAGGGATTCACAGGAGGCCCTTGCTCCACTGgtaagataatttccccgtccttttgatttacagagctgaatatactaggggtgaagaaacatttggatcatcatccattaccacctctaagaatcagatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaca