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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttcaccagtattcagattactatttttgcatggattaaacaggtttatgcttcaatggatgtttgaaaatgtgtggtttgattttatctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACC

Basic information

species Zea mays
transcript GRMZM2G158918_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158918_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g34640.1 (Oryza sativa), 3'ss of exon 3
tattttcaccagtattcagattactattttt-gcatggattaa--acaggtttatgcttcaat---ggatgtttgaaaatgtgtggtttgattttatctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACC
          |  || ||  ||  |||     |  |  ||| |   ||  || || || ||||    |  ||||  |||  | || | || ||    || | ||||  |||||||||||||||||||||||||||| || || ||||||||||| |||||||| | ||| || ||||| | |||||||||||  ||||| ||||||
--ggcatgagaaaatccatttttttatggagaggctaaattgagtgcattttcattctgcaattcaagtcgttttgaaacatctgctatgttt----ctcttacagGAGGCGGCTCTTCAACATGATAAATAACTTACCTACAATATTTGAAGTTGTGACTGGCGCTGCCAAGAAACAGACCAAGGAGAAGGCGCCCAACAGTACC
















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|211514724|gb|FL212193.1|FL212193
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|211512368|gb|FL212178.1|FL212178
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|211514719|gb|FL212188.1|FL212188
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|161588828|gb|EY961990.1|EY961990
EST:     CGGTTTAGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: CGGTTT-GGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|211514714|gb|FL212183.1|FL212183
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAR                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|211512366|gb|FL212176.1|FL212176
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGTCCAG                         ACGGCGGCTCTTCAACATGATAAAT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAAT
EST: gi|211514718|gb|FL212187.1|FL212187
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|211514722|gb|FL212191.1|FL212191
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTYTGGGTT-GACAAAGAGGCCAG                         ACGGCGGCTCTTC
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTC
EST: gi|211514711|gb|FL212180.1|FL212180
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTYTGGGTT-GACAAAGAGGCCAG                         ACGGCGGCTCTTC
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTC
EST: gi|60342605|gb|DN209578.1|DN209578
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|60355178|gb|DN222151.1|DN222151
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|33098649|gb|CF058609.1|CF058609
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|60352190|gb|DN219163.1|DN219163
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|211514720|gb|FL212189.1|FL212189
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATA
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATA
EST: gi|211514717|gb|FL212186.1|FL212186
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACT
EST: gi|211517069|gb|FL212195.1|FL212195
EST:     GCAGTTGCATTCTACTTTGCAGMCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACT
EST: gi|211514712|gb|FL212181.1|FL212181
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACCGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATAT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagAC-GGCGGCTCTTCAACATGATAAATAACTTGCCCACGATAT
EST: gi|60345474|gb|DN212447.1|DN212447
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGT
EST: gi|21843468|gb|BQ704049.1|BQ704049
EST:     GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAG                         ACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTA
genomic: GCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTA

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), 33 (downstream exon)
Score: 241

AGAAGGATTGGTTAGCGCTAGTTGCTGTCCACAGCGATTCCTGGTTACTAGCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACC


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 132

AGAAGGATTGGTTAGCGCTAGTTGCTGTCCACAGCGATTCCTGGTTACTAGCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACC


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 90

AGAAGGATTGGTTAGCGCTAGTTGCTGTCCACAGCGATTCCTGGTTACTAGCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACC


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 87

AGAAGGATTGGTTAGCGCTAGTTGCTGTCCACAGCGATTCCTGGTTACTAGCAGTTGCATTCTACTTTGCAGCCCGGTTTGGGTTTGACAAAGAGGCCAGgtaacggttc ... tctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttatgcttcaatggatgtttgaaaatgtgtggtttgattttatctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACC
                                  gtttgat  putative branch site (score: 87)
                                        ttttatcttt  CT-rich tract
                                   tttgattttatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttcaccagtattcagattactatttttgcatggattaaacaggtttatgcttcaatggatgtttgaaaatgtgtggtttgattttatctttaacagACGGCGGCTCTTCAACATGATAAATAACTTGCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - caccagt
- - - - - - - - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggatg