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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggcagagtgccatttagtaattcttcagtttcagtagcgctagactgttccctgttatggttgtcatgccctgtgatttattgccaagcatgtgttgtagaagaggtaaatcttactagtttctattctttttcctgttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAG

Basic information

species Zea mays
transcript GRMZM2G063676_T01
intron # 8
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|67032698|gb|CO461447.1|CO461447
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|211288524|gb|FL186990.1|FL186990
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGGTTGAGAGAGAGGAAGCA
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGG-TTGAGAGAGAGGAAGCA
EST: gi|31355540|gb|CD439897.1|CD439897
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|24769887|gb|CA405016.1|CA405016
EST:     TGTCCAGTGACCAAAAGTTTGCCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|67011904|gb|CO440653.1|CO440653
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|67029439|gb|CO458188.1|CO458188
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATNCA-TGAGTGCTCTGAAGTNAGA-AACTGGT-GAGAGAAAGGAA-C
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCAT-CAATGAGTGCTCTGAAGT-AGAGAACTGGTTGAGAGAGAGGAAGC
EST: gi|71759979|gb|DR957916.1|DR957916
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|71307555|gb|DR789996.1|DR789996
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|211288523|gb|FL186989.1|FL186989
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTTCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|211148733|gb|FL276359.1|FL276359
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|60396368|gb|DN229237.1|DN229237
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|211288522|gb|FL186988.1|FL186988
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAA                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGNAG-AAGCA
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAG-AGGAAGCA
EST: gi|211148736|gb|FL276362.1|FL276362
EST:     TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
EST: gi|211352366|gb|FL462348.1|FL462348
EST:     TGAGAAACAGAAG                         GTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG
genomic: TGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAG

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: 227

CTCTGTAGATCAACTGGTCTACTGCATCAACAGTTTCAGAGAGGCTGCTTTGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

CTCTGTAGATCAACTGGTCTACTGCATCAACAGTTTCAGAGAGGCTGCTTTGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

CTCTGTAGATCAACTGGTCTACTGCATCAACAGTTTCAGAGAGGCTGCTTTGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

CTCTGTAGATCAACTGGTCTACTGCATCAACAGTTTCAGAGAGGCTGCTTTGTCCAGTGACCAAAAGTTTGGCCATATCGACATATCTGAGAAACAGAAGgtagggcaga ... ttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtagaagaggtaaatcttactagtttctattctttttcctgttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAG
                 atcttac  putative branch site (score: 127)
                           tttctattctttttcc  putative PPT
                           tttctattcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggcagagtgccatttagtaattcttcagtttcagtagcgctagactgttccctgttatggttgtcatgccctgtgatttattgccaagcatgtgttgtagaagaggtaaatcttactagtttctattctttttcctgttgcacacagGTCATCAATGAGTGCTCTGAAGTAGAGAACTGGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT