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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataactcgattgtctccctaatctttttgtaactatcaccttgcttcctcagtatctaactgtcttctcttgggttgtcttatttcctctccccgacaaatcacttccatctactctgggcttttgactttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG

Basic information

species Zea mays
transcript GRMZM2G042027_T05
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 3'ss of exon 9
gtataactcgattgt-ctccctaatctttttgtaactatcaccttgcttcctcagtatctaactgtcttctcttgggttgtcttatttcctctccccgacaaatcacttccatctactctgggcttttgactttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG
|||  |||  ||| |  | | |  ||  ||| |||      ||||| |          | |  | |||  ||||  |||| | |  ||| | |      |      |||| ||   |  |   | |||  |||| ||||||| ||||| ||||| ||||||||||| || || ||||| ||||||||  | ||||||||||||
gtaggactaaattctgtttcttcctcactttctaat-----ccttgttg-------gacaatttttctgttcttatgttgccgtccttcttttgtttacc----tgcttctataacccat---cattt--ctttctgctagGTGCCATTACTGGGGCTATAACAACACCACTCGATGTGATGAAGACGCGGTTGATGGTTCAG

upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA05G31870.1 (Glycine max), 3'ss of exon 10
gtataactcgattgtctccctaatctttttgtaactatcaccttgcttcctcagtatctaactgtcttctcttgggttgtcttatttcctctccccgacaaatcacttccatctactctgggcttttgactttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG
                         || ||| |  ||| |  |   ||          | | ||   | |    |     || |   |||  |   || |  | |||   | || |  ||          ||| |  |||| ||  | |||||||||||||| || |||||||||||||| |||||||| || |||||||| 
------------------------attcttggaggtataagttgctttttgttaagcattattgcaatttgcaagtccaactaa---ccttgcgttgaaatgtgact---aactgccttg----------tttcttgtagGTGCACTAACTGGAGCTATAACTACCCCCCTTGATGTCATCAAGACAAGGTTAATGGTTCAA

upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G15150.1 (Glycine max), 3'ss of exon 9
gtataactcgattgtctccctaatctttttgtaactatcaccttgcttcctcagtatctaactgtcttctcttgggttgtcttatttcctctccccgacaaatcacttccatctactctgggcttttgactttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG
                               |||  ||  | ||| ||  |   | |||   ||| || | |||    |  ||||| | | |||   || |  |  |    |  | | ||      | | ||  || |||| ||  | |||||||||||||| || |||||||||||||| |||||||| || |||||||| 
-------------------------------taa--attgctttgttt--tggttttctgtatgt-ttattttgttaagcattattgcatgtcc--aactagcc-ttgtgttgaaatgtgactgccttatttcctg-tagGTGCACTAACTGGAGCTATAACTACCCCCCTTGATGTCATCAAGACAAGGTTAATGGTTCAA

upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 9
lower sequence: Vv18s0157g00180.t01 (Vitis vinifera), 3'ss of exon 9
gtataactcgattgtctccctaatctttttgtaactatcaccttgcttcctcagtatctaactgtcttctcttgggttgtcttatttcctctccccgacaaatcacttccatctactctgggcttttgactttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG
                               |||  |    || |  ||   |   || || |||| | |  ||  |  |  |   | |||| |  |    |     | |||| | |||   | |||  ||       ||| || || || ||||||||||| ||||| |||||||| || ||||| ||||| |||||||||
------------------------------ctaagaagttactaggatcggtaac-tcaaattgtcatttaatgcat-ataatgcatgctctgcttgtatgagattcttcatcaaatct---cctttatctac-----agGTGCAATAACAGGAGCTATAACTACTCCTCTTGATGTGATAAAGACTAGATTAATGGTTCAG

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|28984641|gb|BQ539144.2|BQ539144
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|113702185|gb|EE679689.1|EE679689
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|91056577|gb|EB166995.1|EB166995
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|71302083|gb|DR787129.1|DR787129
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGA
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGA
EST: gi|76011416|gb|DT938586.1|DT938586
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|16918359|gb|BM073712.1|BM073712
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|71302081|gb|DR787128.1|DR787128
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|78092776|gb|DV521150.1|DV521150
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|211226520|gb|FL435621.1|FL435621
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|33092443|gb|CF052437.1|CF052437
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACCCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|113702087|gb|EE679591.1|EE679591
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|50325363|gb|CO520489.1|CO520489
EST:     AAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: AAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|60342707|gb|DN209680.1|DN209680
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATA
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATA
EST: gi|91054196|gb|EB164614.1|EB164614
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACA
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACA
EST: gi|67018887|gb|CO447636.1|CO447636
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
EST: gi|78083391|gb|DV511784.1|DV511784
EST:     GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG                         GCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT
genomic: GAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGAT

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: 70

GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 31

GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTGgtataactcg ... tttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctctccccgacaaatcacttccatctactctgggcttttgactttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG
                                      ttttgac  putative branch site (score: 31)
                                            ctttttgct  CT-rich tract
                                           acttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataactcgattgtctccctaatctttttgtaactatcaccttgcttcctcagtatctaactgtcttctcttgggttgtcttatttcctctccccgacaaatcacttccatctactctgggcttttgactttttgctagGCGCCATCACTGGAGCTATAACAACTCCCCTTGATGTCATGAAGACAAGATTGATGGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA