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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctactatgctgttgcctatgatgaacaatggatcatacactgcacttgtttcattttttgttctgttggaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTAGTTTACATTG

Basic information

species Zea mays
transcript GRMZM2G159388_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159388_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g12650.1 (Oryza sativa), 3'ss of exon 3
gtatgtctactatgctgttgcctatgatgaacaatggatcatacactgcacttgtttcattttttgttctgttggaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTAGTTTACATTG
||||||||   ||||| |||  | ||   ||  || | ||  | |    |||   |  |||| |  |         |  ||||||| ||||||||  |||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||
gtatgtctgtgatgcttttgtgtttgtataattattgttcccatagcaaactgaat--atttatgatctataccacacttttagGTGATTGCTGGCCTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTGGTTTATATTG
















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|60395326|gb|DN228195.1|DN228195
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|37377979|gb|CF625638.1|CF625638
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|60396291|gb|DN229160.1|DN229160
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|83278714|gb|DV942722.1|DV942722
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|37377329|gb|CF625261.1|CF625261
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|71319886|gb|DR796701.1|DR796701
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|213170374|gb|FM192501.1|FM192501
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|16927724|gb|BM080793.1|BM080793
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|32913287|gb|CF018099.1|CF018099
EST:     ACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: ACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|50330316|gb|CO525442.1|CO525442
EST:     GAAGTTCCTAATG                         GTTATTGCTGCGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: GAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|76915379|gb|DV165957.1|DV165957
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|29576879|gb|CB616991.1|CB616991
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|113701183|gb|EE678687.1|EE678687
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|211035915|gb|FK990122.1|FK990122
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|76915381|gb|DV165958.1|DV165958
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|87156881|gb|DY401670.1|DY401670
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|60400948|gb|DN233755.1|DN233755
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|29945717|gb|CB815783.1|CB815783
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTCCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|32911558|gb|CF016370.1|CF016370
EST:     GATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: GATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|60345750|gb|DN212723.1|DN212723
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|32805271|gb|CD957507.1|CD957507
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|60395367|gb|DN228236.1|DN228236
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|4886126|gb|AI677246.1|AI677246
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|60396494|gb|DN229363.1|DN229363
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|29544868|gb|CB605476.1|CB605476
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|71319888|gb|DR796702.1|DR796702
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|86470074|gb|DY236444.1|DY236444
EST:     AAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: AAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|6564128|gb|AW231750.1|AW231750
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|5928921|gb|AW056213.1|AW056213
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGTTTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|60353543|gb|DN220516.1|DN220516
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|60359185|gb|DN226158.1|DN226158
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
EST: gi|67017360|gb|CO446109.1|CO446109
EST:     CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATG                         GTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC
genomic: CCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 647

AGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTAGTTTACATTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 337

AGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTAGTTTACATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

AGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTAGTTTACATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

AGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTCCGCCAGATTGCTCTTGGCCGGGACCTAAAGAAGTTCCTAATGgtatgtctac ... gaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTAGTTTACATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaatggatcatacactgcacttgtttcattttttgttctgttggaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTAGTTTACATTG
                      ttgtttcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctactatgctgttgcctatgatgaacaatggatcatacactgcacttgtttcattttttgttctgttggaaaatttagGTTATTGCTGGGTTTTGGTTGCTTTCTGTTCTTGGAAGCTGCTGCAACTTCTTGACCTTAGTTTACATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC