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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcactccaaagtttgaagcaagtcatcgcggacatgaattttttttatagtcaaatcgtcctgcatttggttgctgagatgtgttcgttaatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGAAGCTCACAGCTGAGGACCTGAAGGAAATTGGCAGCCAGATACGTGCAGA

Basic information

species Zea mays
transcript GRMZM2G176903_T01
intron # 5
splice site 3'
intron type U2

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|71769569|gb|DR967506.1|DR967506
EST:     AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|211251481|gb|FL481726.1|FL481726
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|33098253|gb|CF058213.1|CF058213
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|76283460|gb|DV023028.1|DV023028
EST:     AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|60394069|gb|DN226939.1|DN226939
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|91052484|gb|EB162902.1|EB162902
EST:     AGCTCTAGCCTGGGTTTTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|67012842|gb|CO441591.1|CO441591
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|32848356|gb|CD988037.1|CD988037
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|93011745|gb|EB637265.1|EB637265
EST:     AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|61119403|gb|DN560364.1|DN560364
EST:     AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|32846945|gb|CD986626.1|CD986626
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|211319907|gb|FL198305.1|FL198305
EST:     GCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: GCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|44901166|gb|CK827711.1|CK827711
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|32845792|gb|CD985473.1|CD985473
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|32834641|gb|CD974319.1|CD974319
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|71763494|gb|DR961431.1|DR961431
EST:     AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|71313076|gb|DR793065.1|DR793065
EST:     AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|71305514|gb|DR788900.1|DR788900
EST:     AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|37391841|gb|CF633165.1|CF633165
EST:     AGCTCTAGCCTGGGTTCTGCATCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|91877438|gb|EB407395.1|EB407395
EST:     AGCTCTAGCCTGGGTTTTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
EST: gi|211387055|gb|FL031624.1|FL031624
EST:     AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAG                         GGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA
genomic: AGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGA

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: 329

CTGAAAATAGAAGATTTGGCGAAGAAGTACCAGTGCAGCCCAGCTCAGCTAGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGAAGCTCACAGCTGAGGACCTGAAGGAAATTGGCAGCCAGATACGTGCAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 176

CTGAAAATAGAAGATTTGGCGAAGAAGTACCAGTGCAGCCCAGCTCAGCTAGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGAAGCTCACAGCTGAGGACCTGAAGGAAATTGGCAGCCAGATACGTGCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 170

CTGAAAATAGAAGATTTGGCGAAGAAGTACCAGTGCAGCCCAGCTCAGCTAGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGAAGCTCACAGCTGAGGACCTGAAGGAAATTGGCAGCCAGATACGTGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

CTGAAAATAGAAGATTTGGCGAAGAAGTACCAGTGCAGCCCAGCTCAGCTAGCTCTAGCCTGGGTTCTGCGTCAAGGGGATGATGTGGTTCCTATACCAGgtgtgacctt ... aatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGAAGCTCACAGCTGAGGACCTGAAGGAAATTGGCAGCCAGATACGTGCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagtcaaatcgtcctgcatttggttgctgagatgtgttcgttaatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGAAGCTCACAGCTGAGGACCTGAAGGAAATTGGCAGCCAGATACGTGCAGA
                                         cgttaat  putative branch site (score: 253)
                                               tttctc  CT-rich tract
                                           ttaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcactccaaagtttgaagcaagtcatcgcggacatgaattttttttatagtcaaatcgtcctgcatttggttgctgagatgtgttcgttaatttctcagGGACAACAAAAACGAAGAACCTAGATGCCAACGTTGACTCCTTGAAGGTGAAGCTCACAGCTGAGGACCTGAAGGAAATTGGCAGCCAGATACGTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA