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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccctgcccaaggtcgtgtctttttcatgactcttctgtccaaatcttgtttcaccgtggcgtccctttcttctctccag

Basic information

species Zea mays
transcript GRMZM2G138886_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138886_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g47580.1 (Oryza sativa), 5'ss of exon 2
ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccctgcccaaggtcgtgtct---ttttcatgactcttctgtccaaatcttgtttcaccgtggcgtccctttcttctctccag--------------------------------------------------
| |||| || |||| |  |||||| ||||||||| ||||||||||||||  | ||| |||| | |||  ||||||||||||| |||||  ||||| || | | |      || | |     | ||     |||  ||   |||  |      |   | | |||  ||||||| || |                                                    
AGATGGGGAACCGGAGGCCGCTCAGGGACATCAACAACCTCGTCGGGGCGCCGCCGCACCCGTCCGCGATCGCCAAGAAGCCGATGCTAGAgtaaaccaccgtctccccccgcgccgagaatctcggagatctcgtgaaaaaagataaaa--aagatcgtgtctttttcttcgctgcttcttggatcgagatcccaatcctttgtggtctgttttttcgcttttgtcag
















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|211247234|gb|FL156674.1|FL156674
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211249461|gb|FL156681.1|FL156681
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211249469|gb|FL156689.1|FL156689
EST:     TCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: TCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|148972285|gb|EE023184.2|EE023184
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211249468|gb|FL156688.1|FL156688
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|76283026|gb|DV022594.1|DV022594
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|71319363|gb|DR796428.1|DR796428
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211249467|gb|FL156687.1|FL156687
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|50324450|gb|CO519576.1|CO519576
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|76294034|gb|DV033602.1|DV033602
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211249466|gb|FL156686.1|FL156686
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211004196|gb|FK981412.1|FK981412
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211004197|gb|FK981413.1|FK981413
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|71439376|gb|DR820426.1|DR820426
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|30307157|gb|CD001830.1|CD001830
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|149081651|gb|EE170801.2|EE170801
EST:     GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211249460|gb|FL156680.1|FL156680
EST:     TCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: TCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
EST: gi|211249462|gb|FL156682.1|FL156682
EST:     GTCGGGGCTGCCCCGTACCCCTGCGCCATCGCCAAGAAGCCCATGCTGCA                         GAAGAGCAGAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT
genomic: GTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCAT

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: 230

ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 17

ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG


Block sizes: 39 (upstream exon), 45 (downstream exon)
Score: 13

ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 18

ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccct ... ttctctccagGAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCAgtaatcccctgcccaaggtcgtgtctttttcatgactcttctgtccaaatcttgtttcaccgtggcgtccctttcttctctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC