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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatcttgaatcctgtcacggtgcacggacttgttacctttcagacctatcccatggccacttgacttactggaaccttgtttcttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG

Basic information

species Zea mays
transcript GRMZM2G370852_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g03260.2 (Oryza sativa), 3'ss of exon 9
---------gtg-agaatcttgaatcctgtcacggtgcacggacttgttacctttcagacctatcccatggccacttgacttactggaaccttgtttcttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
          |  | || ||| ||||   ||| | | || | | || | |  |   |   |||  |||||||  |||||||||||  ||     ||  ||||| ||||| |||||||||||||||||||| || || || || || |||||||||
aatttctctatatacaaacttaaatc---tcatgttaca-gtaattctcaagtcata---ctactccatggctgcttgacttactaaaattgctttcattaatgcagGGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 12
-gtgagaatcttgaatcc-tgtcacggtgcacggacttgttacctttcagacctatcccatggccacttgacttactggaaccttgtttcttaatc--cagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
  |  |   | |||||   |||||   |  |    ||| ||   |||      ||     |   | |||||  |   | ||  |  ||  |  ||   |||||||||||||| |||||||||||||||||||||||||| || ||||||
cttaggtgccatgaatatatgtcagcatctatcttcttttttatttttttttataatttttcttctcttgagct-tagaaatttaattgttctatttacagGGAAAGAAGGTCAAAGTTCCCACATTCCTTGTCCCTGCAACCCAAAAG

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 12
--gtgagaatcttgaatcc-tgtcacggtgcacggacttgttacctttcagacctatcccatggccacttgacttactggaaccttgtttcttaatcca--gGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
   | ||   | |||||   ||| |   ||  |   ||| |    | |      | |           |   ||||    ||  |  |  |    | ||  |||||||||||| |||||||||||||| ||||||||||| || ||||||
acttaagtgccatgaatatatgttagcatgtgcattcttttcttttgttttttttttttttctttttttgagctta--aaaatttaatcgcaccgttcacagGGAAAGAAGGTCAAAGTTCCCACATTTCTTGTCCCTGCAACCCAAAAG

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|149051576|gb|EE155676.2|EE155676
EST:     CGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: CGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|37375881|gb|CF624420.1|CF624420
EST:     CCGCAAAGGTGTTCTAAGCTTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: CCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|76282892|gb|DV022460.1|DV022460
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|24765664|gb|CA400823.1|CA400823
EST:     CCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTACCACACAAAAG
genomic: CCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|76924561|gb|DV170009.1|DV170009
EST:     GGGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|101395254|gb|EB819557.1|EB819557
EST:     CCGCAAAGGGTGTTTTTACCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: CCGCAAA-GGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|16916456|gb|BM072849.1|BM072849
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|31350830|gb|CD435187.1|CD435187
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|60341015|gb|DN207988.1|DN207988
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|32840107|gb|CD979788.1|CD979788
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|211090106|gb|FL396339.1|FL396339
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|71763036|gb|DR960973.1|DR960973
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|32840106|gb|CD979787.1|CD979787
EST:     GTGGCAAGACTGAGGACTTCCTTG-TGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|211011802|gb|FL408548.1|FL408548
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|149080159|gb|EE169177.2|EE169177
EST:     CAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCTTTGTCCCTGCCACACAAAAG
genomic: CAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|211350370|gb|FL368852.1|FL368852
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|148971978|gb|EE022780.2|EE022780
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|74246484|gb|DT654398.1|DT654398
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|149079940|gb|EE168953.2|EE168953
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
EST: gi|211524232|gb|FL397627.1|FL397627
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAACCTCG                         GGAAAAAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCCCACAAAAGG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGG
EST: gi|37418663|gb|CF647003.1|CF647003
EST:     GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
genomic: GTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG

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: 89

AGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 145

AGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

AGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

AGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACTTCCTTGCTGCCGCAAAGGTGTTCTTAGCCTCGgtgagaatct ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagacctatcccatggccacttgacttactggaaccttgtttcttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG
                                     ccttgtttctt  CT-rich tract
                                          tttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaatcttgaatcctgtcacggtgcacggacttgttacctttcagacctatcccatggccacttgacttactggaaccttgtttcttaatccagGGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG