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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattggatactgttcattttactttactttgtatggcctagcacttgtattgatgtatcacttaaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA

Basic information

species Zea mays
transcript GRMZM2G107867_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 9
gtattggatactgttca-ttttactttactttgtatggc---ctagcacttgtattgatgtat--cacttaaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA
|| ||| ||  |||||  |||||||     || | || |   ||   | ||||  ||| ||||  |||||| |||||||||||| || || ||||| || |||||| |||||||| |||| |||||| |||| ||||| ||| | |||||||||||||| || |||||| |||| ||||
gtcttgcatgatgttctcttttactactacttttgtgacacactgaaatttgtgctgacgtatatcacttatccaacagTCTCGAGCTCAGCCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTGAAGACTTAAATGTCTGCTGGAAGAAGAATGGACAGTACAACATGAAGTGCA

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 9
gtattggatactgttcattttactttactttgtatggc-ctagcacttgtattgatgtatcacttaaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA
|| ||| ||  ||||| ||||   ||  ||||||   | |    | ||||| |||  ||||| ||| ||||||||| || || || ||||| || |||||| |||||||| |||| ||||||||||| ||||| |||   |||||||||||||| || |||||| |||||||||
gttttgcatgatgttcctttttacttcttttgtaacacaccgaaatttgtactgacatatcaattatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAAGACTTAAATGTCTCCTGGAAGAAGAATGGACAGTACAACATGAAATGCA

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 9
--------------------gtattggatactgttcattttactttactttgtatggccta---gcacttgtat-tgatgtatcacttaacc---aacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA
                    ||| | | | |  |       | | || |||  ||| | |    | | || |||    | | |   ||| |     ||||||||| ||||| |||||||||||||||  ||||||| | |||||  | ||||||||||| ||  | |||||||||| ||| ||||||||| |||| || |
taacggctgtttgaatttttgtaatagttgccatcagaaaaattgtagttttgatgtcttgttggtagttatatactttttgttcattatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 10
-----------------------gtattggatactgttcattttactttactttgtatggcctagcacttgt-attgatgtatcacttaacc---aacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA
                       ||| | |   |  |       | | || | |  ||| | |     | || | | |  | |   ||| |     ||||||||| ||||| |||||||||||||||  ||||||  | |||||  | ||||||||||| ||  | |||||||||| ||| ||||||||| |||| || |
atatctaaaagctgtttgtttttgtaatagtggccatcagaaaaattgtagtcttgatgtcttgttggtagttacttactttttgtttatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTTCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
-------------------gtattgga-tactgttcattttacttta----ctttgtatggcctagcacttgtattgatgtatcacttaacc---aacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA
                    ||||| | | ||| |    ||| |||      |   | || |  ||  |||   | | | | |   |||||     | ||||||| ||||| || ||||||||||||  ||||||| | ||||| || ||||||||||| ||  | |||||||||| ||| ||||| ||| |||| ||||
ttattaatggttatcagaaatattgaagttctgatgtacttattttgatggttacttgtgactgaggtctttgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA

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|6031419|gb|AW076321.1|AW076321
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|211186172|gb|FL452293.1|FL452293
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|60341419|gb|DN208392.1|DN208392
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|5871760|gb|AW018231.1|AW018231
EST:     CGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: CGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|91872727|gb|EB402684.1|EB402684
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|6056642|gb|AW091047.1|AW091047
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|211210980|gb|FL114022.1|FL114022
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|211186173|gb|FL452294.1|FL452294
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|60398350|gb|DN231166.1|DN231166
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|71762342|gb|DR960279.1|DR960279
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
EST: gi|211208425|gb|FL114020.1|FL114020
EST:     GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAG                         TCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA
genomic: GTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAA

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), 46 (downstream exon)
Score: 87

TTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 98

TTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 119

TTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 91

TTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtattggata ... taaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactttactttgtatggcctagcacttgtattgatgtatcacttaaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA
                                          acttaac  putative branch site (score: 91)
     tttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattggatactgttcattttactttactttgtatggcctagcacttgtattgatgtatcacttaaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG