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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtcttgaatatgtatttattgcagtttaatatttggtgttccccttccttagataataattaatccacctaactgatgctgaaatgcctttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG

Basic information

species Zea mays
transcript GRMZM2G063511_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 3
ggtcttgaatatgtatttattgcag---tttaat--atttggtgttccccttccttagataataattaatccacctaactgatgctgaaatg-cctttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG
      | | |    |||||||||    |||| |  | ||| ||| ||| ||| |   | | |||| ||||||||||||| |||| |||||| ||||||| |||||||||| |||||||| |||||||| |||||||| || || ||||| |||||||||||||||||||||||
-----agcacaacattttattgcaagcatttatttcaattgatgtgccctttcttcc-acactaatcaatccacctaacttatgccgaaatgtcctttatgtctagATGACAAAGCTGGCTATCATCCCATGCACTGTTATTTTGGAGACTCTTTTCTTCAGGAAGAAGTTCAG

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 3
ggtcttgaatatgtatttattgcagtt-taatatttggtgttccccttccttagataataattaatcca---cctaactgatgctgaaatgcctttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG
     |  |  | | |  ||| |||||     ||   ||| |  || |  |||  || |  ||  || |    |||||  ||  |    | | || |||  ||||||||||| || || |||||||| ||||||||  |||| ||||| || ||||||||||| ||||||||
----gtatagctttttccatttcagttactgcatgatgtgatatccatttttaactagtg-ttgttctaatttctaacccatcttctgttccgttgataa-tagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAG

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 4
-----------ggtcttgaatatgtatt--tattgca-gtttaatatttggtgttccccttccttaga------taataattaatccacctaactgatgctgaaatgcctttatat-ctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG
             |  |||||||    |  |||| || ||| ||  ||||||  |   |    | ||        || |         |  |||| ||| |  | ||  | | ||| | ||||||| |||||||| ||||| || || |||||  |||| ||||| ||||||||||||||||| |||||
gtaaaattaattcttctgaatattccctactattacatgttcaacttttggtcctttgccatttcagtgtttctcaagagagtggtttctgaacttatgttatattgtttgtgtattccagATGACAAAGCTGGCAATCATTCCCTGTACTGTACTCTTGGAGACCCTTTTCTTCAGGAAGAAATTCAG

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|78113976|gb|DV532365.1|DV532365
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
EST: gi|148991668|gb|EE033210.2|EE033210
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
EST: gi|71303455|gb|DR787837.1|DR787837
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCCACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCGATCATCC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCC
EST: gi|148934066|gb|EC878080.2|EC878080
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
EST: gi|74238674|gb|DT646588.1|DT646588
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
EST: gi|76281072|gb|DV020640.1|DV020640
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
EST: gi|71770743|gb|DR968680.1|DR968680
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
EST: gi|71444391|gb|DR825441.1|DR825441
EST:     TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAG                         ATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC
genomic: TTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTC

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), 48 (downstream exon)
Score: 242

TTTTGATTCAAGAACTGTCATGGGATTTGGAGTACTTAATGGAATCTCCATTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 226

TTTTGATTCAAGAACTGTCATGGGATTTGGAGTACTTAATGGAATCTCCATTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

TTTTGATTCAAGAACTGTCATGGGATTTGGAGTACTTAATGGAATCTCCATTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 301

TTTTGATTCAAGAACTGTCATGGGATTTGGAGTACTTAATGGAATCTCCATTGGGCTCCTCAACTTGAGTCTTGGCTTCAACTCTGTTGGGTTTTACCAGgtatagacat ... ttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttagataataattaatccacctaactgatgctgaaatgcctttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG
                                        tgccttt  CT-rich tract
     tagataataattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtcttgaatatgtatttattgcagtttaatatttggtgttccccttccttagataataattaatccacctaactgatgctgaaatgcctttatatctagATGACTAAGCTGGCGATCATCCCGTGCACTGTCATCTTAGAGACACTTTTCTTCAGGAAGAAGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - atatgta
- - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcct