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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactgtaaccgttgtacattaacaatacaaggcagaggatgccaatctcagataatgtcgttccaatttcacctttttttttgcttttgtggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 1
splice site 3'
intron type U2

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|22542184|gb|BU092622.1|BU092622
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|148958443|gb|EC904677.2|EC904677
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|148995832|gb|EE035067.2|EE035067
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211347818|gb|FL132814.1|FL132814
EST:     GCCTCATGGACCTCCCACAGGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GCCTCATGGACCTCCCACA-GGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211345429|gb|FL132812.1|FL132812
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|149076511|gb|EE165137.2|EE165137
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|87157287|gb|DY402076.1|DY402076
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|149086279|gb|EE175820.2|EE175820
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|149107582|gb|EE189463.2|EE189463
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|71430909|gb|DR811959.1|DR811959
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|149073920|gb|EE162247.2|EE162247
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|149098382|gb|EE184358.2|EE184358
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211174083|gb|FL129198.1|FL129198
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211345428|gb|FL132811.1|FL132811
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|148942583|gb|EC887602.2|EC887602
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|9254572|gb|BE345040.1|BE345040
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGGTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|26559314|gb|CA831549.1|CA831549
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211174080|gb|FL129195.1|FL129195
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|93282461|gb|EB674725.1|EB674725
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|149085816|gb|EE175338.2|EE175338
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|148970227|gb|EE021164.2|EE021164
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|148999540|gb|EE036511.2|EE036511
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211347820|gb|FL132816.1|FL132816
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|76283292|gb|DV022860.1|DV022860
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211175751|gb|FL129202.1|FL129202
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211174081|gb|FL129196.1|FL129196
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|211175754|gb|FL129205.1|FL129205
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
EST: gi|94479494|gb|EB708452.1|EB708452
EST:     GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAG                         TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT
genomic: GGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGT

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: 305

CCGGCAGGCCGTCGGCCGGGCCCGTGTACCGGAGCATCTACGCCAAGGACGGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

CCGGCAGGCCGTCGGCCGGGCCCGTGTACCGGAGCATCTACGCCAAGGACGGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG


Block sizes: 12 (upstream exon), 38 (downstream exon)
Score: 1

CCGGCAGGCCGTCGGCCGGGCCCGTGTACCGGAGCATCTACGCCAAGGACGGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 726

CCGGCAGGCCGTCGGCCGGGCCCGTGTACCGGAGCATCTACGCCAAGGACGGCCTCATGGACCTCCCACAGGACATCCAGTCCCCTTGGGACTTGTTCAGgtccggtccc ... ggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcagataatgtcgttccaatttcacctttttttttgcttttgtggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG
                            tttttttttgctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactgtaaccgttgtacattaacaatacaaggcagaggatgccaatctcagataatgtcgttccaatttcacctttttttttgcttttgtggtctcgtagTGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - ggatgcc