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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattatgatgaacagtcttgcagtatcgcgacttaatctcccaaccgcacatgtattcagttcctggcaccaagactgattatggtgaacatttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAAAGTCACCTCTTCTACAACATGACGTCGCTGCTGTGGAAGGGCATTCATC

Basic information

species Zea mays
transcript GRMZM2G053066_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053066_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g18100.1 (Oryza sativa), 3'ss of exon 1
gattatgatgaacagtcttgcagtatcgcgacttaatctcccaaccgcaca-tgtattcagttcctggcaccaagactgattatggtgaacatttt--tgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAAAGTCACCTCTTCTACAACATGACGTCGCTGCTGTGGAAGGGCATTCATC
        |      || | ||   ||     ||| | |    |    ||| | |  |   | |     || |||   ||| || ||      |||  |||||||  | ||| |||| ||||| ||||||||  | |||||||||||||| |||| |||| |||||| ||||||| | || ||  | ||||||||||| || |
--ccccatttggatttcctacaccttc-tattttattgttttgaagttacagtctgctggttccacctgactaagcaagatgatcgttgttggtttgttgcagTACTGTGACCTGACACGCTTCTTCCTGTCGGCTTTCTACCACTTGAGCGAAACTCACTTCTTCTTCAACATGTCATCTCTCTTATGGAAGGGCATCCAGC
















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|78079412|gb|DV507824.1|DV507824
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|93013857|gb|EB639377.1|EB639377
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|50338656|gb|CO533782.1|CO533782
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|74239420|gb|DT647334.1|DT647334
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|211062057|gb|FL354581.1|FL354581
EST:     TCCTGCCCTCTCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACG
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACG
EST: gi|149049750|gb|EE048434.2|EE048434
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|88756612|gb|DY540753.1|DY540753
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|78089632|gb|DV518006.1|DV518006
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|50328178|gb|CO523304.1|CO523304
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|76015067|gb|DT942237.1|DT942237
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|50335716|gb|CO530842.1|CO530842
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTT-CTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|67016083|gb|CO444832.1|CO444832
EST:     TCCTGCCCTCGCTGGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTCTTACTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|148939606|gb|EC884236.2|EC884236
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|101382373|gb|EB813242.1|EB813242
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|148958315|gb|EC904537.2|EC904537
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
EST: gi|37424582|gb|CF650024.1|CF650024
EST:     TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAG                         TATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA
genomic: TCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAA

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: 36 (upstream exon), 44 (downstream exon)
Score: 8

GCTCGCCGCCAACTCACTCGTCTACCTCCGCCCCGGCGCGCTCGACGGGGTCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAAAGTCACCTCTTCTACAACATGACGTCGCTGCTGTGGAAGGGCATTCATC


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 23

GCTCGCCGCCAACTCACTCGTCTACCTCCGCCCCGGCGCGCTCGACGGGGTCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAAAGTCACCTCTTCTACAACATGACGTCGCTGCTGTGGAAGGGCATTCATC


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 19

GCTCGCCGCCAACTCACTCGTCTACCTCCGCCCCGGCGCGCTCGACGGGGTCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAAAGTCACCTCTTCTACAACATGACGTCGCTGCTGTGGAAGGGCATTCATC


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 11

GCTCGCCGCCAACTCACTCGTCTACCTCCGCCCCGGCGCGCTCGACGGGGTCCTGCCCTCGCTCGCGCGCGTCTCCTTCAACCCTCAGCTCATCATCGAGgtgcctgacc ... atttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAAAGTCACCTCTTCTACAACATGACGTCGCTGCTGTGGAAGGGCATTCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcacatgtattcagttcctggcaccaagactgattatggtgaacatttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAAAGTCACCTCTTCTACAACATGACGTCGCTGCTGTGGAAGGGCATTCATC
                            gactgat  putative branch site (score: 11)
                                            cattttt  putative PPT
                                          aacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattatgatgaacagtcttgcagtatcgcgacttaatctcccaaccgcacatgtattcagttcctggcaccaagactgattatggtgaacatttttgcagTATGGCGACTTGACGCGCTTTTTCCTGTCACCCTTCTACCACTTGAGTGAAAGTCACCTCTTCTACAACATGACGTCGCTGCTGTGGAAGGGCATTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - -tgatgaa
- - - - - - - -tcttgca
- - - - - - - - - - - - - - - - - - - - ccaaccg
- - - - - - - - - - - - - - - - - - - - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatt