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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgatgccaagtatatcattttaattaatcaagaaaagataaacatttattgttttttctgttcccttgatattttccttggctcttactttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG

Basic information

species Zea mays
transcript GRMZM2G149952_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149952_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------cttgatgccaagtatat-cattttaatt-aatcaagaaaagataaacatttattgttttttctgttcccttga--tattttccttggc-----tcttactttggt---tcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG
                                                                |||  || | |   | | ||||| ||||        ||   | | |  ||  || |    |        |||   | |||| ||||||     || |  |||| |   |||||||||||| |||||||||||||||||||||||||| || || |||||||||||||||||||||||||||||||||||||||||||||
gtatgtcatcctaccagaccagatatcacattttttggatgcactagattgtgtagttcgctagcttactgtccatcttgtacatttgaatttggatgtcaagcaacatattttagttttcagataaaccttgttgtattctttttcttggcatgactcctgatttgttttatcagGTGGCTGCATATGACACAAAGCAAAAGAAAATGGACTTTTTCGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG
















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|166552426|gb|EG143042.1|EG143042
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTA
EST: gi|32920504|gb|CF025316.1|CF025316
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTCGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|32829670|gb|CD969348.1|CD969348
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|32830909|gb|CD970587.1|CD970587
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|37387177|gb|CF630781.1|CF630781
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|149040632|gb|EE046873.2|EE046873
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGGGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|32829388|gb|CD969066.1|CD969066
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|32831393|gb|CD971071.1|CD971071
EST:     CTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: CTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|211229396|gb|FL476090.1|FL476090
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACMCAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|32831832|gb|CD971510.1|CD971510
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|16926603|gb|BM079671.1|BM079671
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|76287850|gb|DV027418.1|DV027418
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|60342436|gb|DN209409.1|DN209409
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|37390063|gb|CF632257.1|CF632257
EST:     GAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTACAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATC
genomic: GAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTT-CAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATC
EST: gi|32829476|gb|CD969154.1|CD969154
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|60345908|gb|DN212881.1|DN212881
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|32829296|gb|CD968974.1|CD968974
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|60357535|gb|DN224508.1|DN224508
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
EST: gi|32831003|gb|CD970681.1|CD970681
EST:     TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAG                         GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA
genomic: TTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCA

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: 95

CCACCCCACAGAGAAAAGGGACCTCTATGATGCTGATCACGGAAAGAAGGTTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1665

CCACCCCACAGAGAAAAGGGACCTCTATGATGCTGATCACGGAAAGAAGGTTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1453

CCACCCCACAGAGAAAAGGGACCTCTATGATGCTGATCACGGAAAGAAGGTTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

CCACCCCACAGAGAAAAGGGACCTCTATGATGCTGATCACGGAAAGAAGGTTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgtatgtcatc ... tttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattgttttttctgttcccttgatattttccttggctcttactttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG
                                      ctcttac  putative branch site (score: 173)
                                      ctcttacttt  CT-rich tract
                      ttgatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgatgccaagtatatcattttaattaatcaagaaaagataaacatttattgttttttctgttcccttgatattttccttggctcttactttggttcagGTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- tgatgcc
- - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - gataaaca