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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagatctacatccctttttctattggttaagtgaaatctaggcactgtacttgtcctgtgatcctgactgtcaaattggcatgtattttgtggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG

Basic information

species Zea mays
transcript GRMZM2G117707_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117707_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g42960.2 (Oryza sativa), 3'ss of exon 2
gtcagatctacatccctttttctattggttaagtgaaatctaggcactgtac---ttgtcctgtg-atcctgac-tgtcaaattggcatgtattttgtggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG
|||||   |   |   ||||  ||   |||| ||||||||       |||      || | |||| ||  |||| | ||||| || |||  |   |||| |||||||||||| ||||||||||||||| |||||||||||||||| ||||||||| ||||||| |||||||| ||||||||||| |||||||||||||| |||||||
gtcagcattgagtttattttcataa-agttatgtgaaatcctaatgttgtttgcagtgccttgtggatgttgacatttcaaactgacattgaccctgtgtaatgtagGTGAGTGACAAAATGAACCCCCGTGACTTGGTGAAGCTCATTGAGATTTTGAACCCATCAAACAAGCCTGGAAGGATAACCATAATTACAAGAATGGGGG
















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|76291136|gb|DV030704.1|DV030704
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|32849969|gb|CD989650.1|CD989650
EST:     GAGCGCATGTTGAATTCCTTCGCGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|32850166|gb|CD989847.1|CD989847
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCCGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|78092820|gb|DV521194.1|DV521194
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|61118358|gb|DN559319.1|DN559319
EST:     CCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: CCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|32837625|gb|CD977303.1|CD977303
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|67030191|gb|CO458940.1|CO458940
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|78117894|gb|DV536281.1|DV536281
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|61118357|gb|DN559318.1|DN559318
EST:     CCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: CCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|32848606|gb|CD988287.1|CD988287
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|37416855|gb|CF646079.1|CF646079
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|78108038|gb|DV526456.1|DV526456
EST:     TCCTTCCGTGGTG-TGCCCATCCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: TCCTT-CGTGGTGTTGCCAAT-CCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|24934562|gb|CA452780.1|CA452780
EST:     GAGCGCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|32850081|gb|CD989762.1|CD989762
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACANAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|32849069|gb|CD988750.1|CD988750
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGTCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|78082881|gb|DV511274.1|DV511274
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|76019203|gb|DT946373.1|DT946373
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|32920110|gb|CF024922.1|CF024922
EST:     GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|24934601|gb|CA452819.1|CA452819
EST:     GAGCGCATGTTGAATTCCTCCGTGGTGTTGCCAACCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
EST: gi|32850168|gb|CD989849.1|CD989849
EST:     GAGCGCATGTTGAATTCCTTCGTGGGGTTGCCAATCCTCTTGGCATAAAG                         GTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG
genomic: GAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTG

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: 304

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGTCAACTCGATGGAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 437

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGTCAACTCGATGGAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 625

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGTCAACTCGATGGAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1078

TTGTTCGGCCCACATGTTGTGGGTTGGTGAGCGCACTCGTCAACTCGATGGAGCGCATGTTGAATTCCTTCGTGGTGTTGCCAATCCTCTTGGCATAAAGgtcagatcta ... tggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacttgtcctgtgatcctgactgtcaaattggcatgtattttgtggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG
                tcctgac  putative branch site (score: 1078)
                                   atgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagatctacatccctttttctattggttaagtgaaatctaggcactgtacttgtcctgtgatcctgactgtcaaattggcatgtattttgtggaatgtagGTGAGCGACAAAATGAACCCCAGTGACTTGGTGAAGCTGATTGAGATTCTGAACCCTTCAAACAAACCTGGAAGGATCACCATAATTACAAGGATGGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG