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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctgacacttgtactatgtttttagctgttcaccggtgattgggagagttctatctgacatgatacactgatcaaaatctaccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA

Basic information

species Zea mays
transcript GRMZM2G438551_T02
intron # 3
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|74035349|gb|DT535838.1|DT535838
EST:     GTTGTGGCCACAGCCCCGGCTCTCGCAG                         GATCTGTCGTCCTCCCTGGGCAAATTTTGCTGCCCTGAAAGCGCAAAACTA
genomic: GTTGTGGCCACAGCCC-GGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTC-TCCCTGTGCAA-TTT-GCTGCC-TGAA-GCGCAAAACTA
EST: gi|211035017|gb|FL300564.1|FL300564
EST:     GTTGTGGCCACAGCCCGGCTCTCGCAG                         GATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
genomic: GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
EST: gi|71595831|gb|DR906582.1|DR906582
EST:     GTTGTGGCCACAGCCCGGCTCTCGCAG                         GATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
genomic: GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
EST: gi|74237713|gb|DT645627.1|DT645627
EST:     GTTGTGGCCACAGCCCGGCTCTCGCAG                         GATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
genomic: GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
EST: gi|211030097|gb|FL300540.1|FL300540
EST:     GTTTTGGCCACAGCCCGGCTCTCGCAG                         GATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
genomic: GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
EST: gi|161580268|gb|EY954953.1|EY954953
EST:     CGGCTCTCGCAG                         GATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAAACTAAGTT
genomic: CGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAA-CTAAGTT
EST: gi|21621004|gb|BQ619010.1|BQ619010
EST:     GTTGTGGCCACAGCCCGGCTCTCGCAG                         GATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
genomic: GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG
EST: gi|71596322|gb|DR907073.1|DR907073
EST:     GTTGTGGCCACAGCCCGGCTCTCGCAG                         GATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTTAGTTG
genomic: GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTG

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 8 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 5

GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2146

GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 3

GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1247

GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 8

GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 736

GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA


Block sizes: 48 (upstream exon), 26 (downstream exon)
Score: 3

GTTGTGGCCACAGCCCGGCTCTCGCAGgtcctgacac ... ccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgggagagttctatctgacatgatacactgatcaaaatctaccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA
                             cactgat  putative branch site (score: 3)
                                  atcaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctgacacttgtactatgtttttagctgttcaccggtgattgggagagttctatctgacatgatacactgatcaaaatctaccaattgcagGATCTGTCGTCTCCCTGTGCAATTTGCTGCCTGAAGCGCAAAACTAAGTTGCAGAATAAGGAGCTGCTTCGGAACATGCCAGAGCATGCACCCTCGCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA