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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagttttgctgcgtgcagttaccaatttattcaccgttgaggatcatgagctttgcttctgattatctcacttatcttgttttgtttgccattgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG

Basic information

species Zea mays
transcript GRMZM2G101217_T03
intron # 10
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|50337134|gb|CO532260.1|CO532260
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|93012640|gb|EB638160.1|EB638160
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAG                         GATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG
EST: gi|71418851|gb|DR804567.1|DR804567
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|50336105|gb|CO531231.1|CO531231
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|71763051|gb|DR960988.1|DR960988
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAG                         A
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaag-
EST: gi|71763051|gb|DR960988.1|DR960988
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAG                         A
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaag-
EST: gi|71763051|gb|DR960988.1|DR960988
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAG                         A
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaag-
EST: gi|50325601|gb|CO520727.1|CO520727
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|76281531|gb|DV021099.1|DV021099
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|148960596|gb|EE011218.2|EE011218
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|60352980|gb|DN219953.1|DN219953
EST:     ACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: ACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|76924071|gb|DV169789.1|DV169789
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga

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 2 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 2

ACATCAAGCTTTACCGAGCATGTCCCTTATTGCTTCAGACTTCAGCTATCTTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 3

ACATCAAGCTTTACCGAGCATGTCCCTTATTGCTTCAGACTTCAGCTATCTTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgagctttgcttctgattatctcacttatcttgttttgtttgccattgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG
                   atctcac  putative branch site (score: 3)
                                  ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagttttgctgcgtgcagttaccaatttattcaccgttgaggatcatgagctttgcttctgattatctcacttatcttgttttgtttgccattgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - -ttgctgc
- - - - - - -tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc