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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctgatctctgactctgatcatgccctttgaactagactgtgttgatttggtgtttgtactttctggttcactaaaatcttttcatcttgtttgtacag

Basic information

species Zea mays
transcript GRMZM2G100620_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100620_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 5'ss of exon 4
ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctgatctctgactctgatcatgc--cctttgaactagactgtgttgatttggtgtttgtactttctggttcactaaaatcttttcatcttgt---ttgtacag
|||||||| |||||||||||||| ||  |||||||||||||||| |||||| ||||||||||||||||||| |  |||       |||||  | |    ||     |    | ||||| |||| |  ||   |       |  ||   || ||      ||  |   ||||||||
ATTGGTTATCCTGAAATTGAAGAAAACAGCAAGCCAAGGCACCGTTTCATGGCATCATATGAACAGgtaaagc-aatcaacctgcctgattgttcggttttcagtttgtggtatgttgctttgtttgttactcccatgtatcaacagtaacctaacagactgatgttttgtacag
















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|19351244|gb|BM895776.1|BM895776
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|149014483|gb|EE044106.2|EE044106
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|19272503|gb|BM888759.1|BM888759
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|211397250|gb|FL247601.1|FL247601
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTTGCAGA
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCT-GCAGA
EST: gi|149111001|gb|EE294500.2|EE294500
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|91056062|gb|EB166480.1|EB166480
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|18648819|gb|BM497638.1|BM497638
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|76292130|gb|DV031698.1|DV031698
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|148944813|gb|EC889958.2|EC889958
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|78092801|gb|DV521175.1|DV521175
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|78077143|gb|DV505577.1|DV505577
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|148937013|gb|EC881184.2|EC881184
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|71439882|gb|DR820932.1|DR820932
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|149111002|gb|EE294501.2|EE294501
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|37417746|gb|CF646533.1|CF646533
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTAC
EST: gi|50330974|gb|CO526100.1|CO526100
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|78113433|gb|DV531825.1|DV531825
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|32863198|gb|CF002880.1|CF002880
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|6564142|gb|AW231764.1|AW231764
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|149081122|gb|EE170228.2|EE170228
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|211402594|gb|FL136251.1|FL136251
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAA-GTTGGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGA
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGG-ATAAGAGGTATCAATACCTACTTTTTGCTGCAGA
EST: gi|32803496|gb|CD955732.1|CD955732
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
EST: gi|18648881|gb|BM497700.1|BM497700
EST:     TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG                         AAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC
genomic: TTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGAC

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: 342

ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 203

ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctga ... gtttgtacagAAAGTCCAAAGTTGGGATAAGAGGTATCAATACCTACTTTTTGCTGCAGACCCCTATGAAATCATTGCATTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAGgtaaacctgatctctgactctgatcatgccctttgaactagactgtgttgatttggtgtttgtactttctggttcactaaaatcttttcatcttgtttgtacag

- - - - - - - - TTGAAG
- - - - - - - -  TGAAGA