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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgctgttgctcgccgtttctgttgcttcttagtcgtatagtgttgctattttacaattttatctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTG

Basic information

species Zea mays
transcript GRMZM2G540403_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 3'ss of exon 7
gtaagtcgc-tgttgctcgccgtttctgttgcttcttagtcgtata-gtgttgctattttacaattttatctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTG
|||||||   ||| ||      |||   |   || ||  |  | ||   |||  | |||     ||| |||||     |||||||||| || ||||| || |||||| | || ||||||||| ||||||| ||||| |||||||| ||||||||||| ||||||||||||||| ||||||
gtaagtcttatgtcgcattttcttttgctaagttatttcttttttacaagttattgtttccatgtttcatctgtcatcagGTTAGCAACCCTGCAATCCAATTCATGTTGTACGAGACTCTTTTGAAGAAGTTGAAAAAGAGACGTGCCTCTAATTTGAAGGGAGCTGATGGACTGACTG
















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|24934302|gb|CA452520.1|CA452520
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
EST: gi|32935002|gb|CF039814.1|CF039814
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCC
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCC
EST: gi|211096941|gb|FL476436.1|FL476436
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTG
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTG
EST: gi|32929640|gb|CF034452.1|CF034452
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
EST: gi|166600046|gb|EG079333.1|EG079333
EST:     TCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: TCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
EST: gi|211285344|gb|FL118293.1|FL118293
EST:     AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG                         GTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA
genomic: AATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAA

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), 48 (downstream exon)
Score: 109

TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 260

TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156

TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATGgtaagtcgct ... ctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttgcttcttagtcgtatagtgttgctattttacaattttatctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTG
                                       ttttatctgcttct  CT-rich tract
                             tattttacaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgctgttgctcgccgtttctgttgcttcttagtcgtatagtgttgctattttacaattttatctgcttctagGTTAGCAATCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA