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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggctggagccttgttgataggagtgcactagttatggtctttttaggtcttcccaggctgagtttctgccataactcaattttgctttcctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGACATGGCCAACAGCCTTGATACTAACTGCACTCCCATTGCTAAAGGATGCA

Basic information

species Zea mays
transcript GRMZM2G328060_T01
intron # 1
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|50323049|gb|CO518175.1|CO518175
EST:     ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCG                         GGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
genomic: ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
EST: gi|76291940|gb|DV031508.1|DV031508
EST:     ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCG                         GGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
genomic: ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
EST: gi|50337791|gb|CO532917.1|CO532917
EST:     ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCG                         GGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
genomic: ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
EST: gi|211266363|gb|FL163926.1|FL163926
EST:     ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCG                         GGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
genomic: ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
EST: gi|149071414|gb|EE159807.2|EE159807
EST:     ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCG                         GGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
genomic: ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
EST: gi|50323633|gb|CO518759.1|CO518759
EST:     ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCG                         GGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
genomic: ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
EST: gi|78086551|gb|DV514944.1|DV514944
EST:     ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCG                         GGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC
genomic: ACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGAC

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: 43 (upstream exon), 45 (downstream exon)
Score: 2

GGGCAGCCGCTCCGTCGTGGTCGGTGCTGGTGGCTCGCCGGCGAGGTGGGACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGACATGGCCAACAGCCTTGATACTAACTGCACTCCCATTGCTAAAGGATGCA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 14

GGGCAGCCGCTCCGTCGTGGTCGGTGCTGGTGGCTCGCCGGCGAGGTGGGACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGACATGGCCAACAGCCTTGATACTAACTGCACTCCCATTGCTAAAGGATGCA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 13

GGGCAGCCGCTCCGTCGTGGTCGGTGCTGGTGGCTCGCCGGCGAGGTGGGACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGACATGGCCAACAGCCTTGATACTAACTGCACTCCCATTGCTAAAGGATGCA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 14

GGGCAGCCGCTCCGTCGTGGTCGGTGCTGGTGGCTCGCCGGCGAGGTGGGACGACGATAACGACGACTGCGGCGGCGGCGGACGTGTCGAAGGCTTGGCGgtaagctccc ... cctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGACATGGCCAACAGCCTTGATACTAACTGCACTCCCATTGCTAAAGGATGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggtcttcccaggctgagtttctgccataactcaattttgctttcctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGACATGGCCAACAGCCTTGATACTAACTGCACTCCCATTGCTAAAGGATGCA
                                            tcctgat  putative branch site (score: 14)
                                    ttttgctttcct  CT-rich tract
                                tcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggctggagccttgttgataggagtgcactagttatggtctttttaggtcttcccaggctgagtttctgccataactcaattttgctttcctgatatagGGACTCCACATATTTGACCAAGAGGCAGAGGAGTCACCAACCAAAAACGACATGGCCAACAGCCTTGATACTAACTGCACTCCCATTGCTAAAGGATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- -gctggag
- - - - - - -tgttgat
- - - - - - - - - - - - -tgcacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactcaa