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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgcacacaaaaaaaaaaaaagataagccactatctgccagctcaagacattgtttgctagcagacgattcttatcggttcctgattgccttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAGTTACAAGGCAGCCACGGCGACACCGTACCTGTGGCTCTCGGCGATGAAG

Basic information

species Zea mays
transcript GRMZM2G170161_T01
intron # 2
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|60341074|gb|DN208047.1|DN208047
EST:     TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAG                         ATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
genomic: TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
EST: gi|76015107|gb|DT942277.1|DT942277
EST:     TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAG                         ATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
genomic: TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
EST: gi|89758783|gb|DY687836.1|DY687836
EST:     TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAG                         ATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
genomic: TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
EST: gi|78113764|gb|DV532153.1|DV532153
EST:     TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAG                         ATTCTGGGAA-CTAGGGGACAAGT-GTCGCAGGAGGTGCGGTACCGGACGG
genomic: TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGG-AAGCTAGGG-ACAAGTTGTCGCAGGAGGTGCGGTACCGGACGG
EST: gi|91048361|gb|EB158779.1|EB158779
EST:     TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAG                         ATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
genomic: TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
EST: gi|71768462|gb|DR966399.1|DR966399
EST:     TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAG                         ATTCTGGAAGCTA
genomic: TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTA
EST: gi|50329757|gb|CO524883.1|CO524883
EST:     TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAG                         ATTCTGGAAGCTAGGGACAAGTT
genomic: TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTT
EST: gi|74232592|gb|DT640506.1|DT640506
EST:     TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAG                         ATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG
genomic: TGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAG

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: 44 (upstream exon), 42 (downstream exon)
Score: 20

CCCCAGCCACATGAGCGAGGACTGCTTCTGGAAGATATACTTCGTACTGCTGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAGTTACAAGGCAGCCACGGCGACACCGTACCTGTGGCTCTCGGCGATGAAG


Block sizes: 41 (upstream exon), 44 (downstream exon)
Score: 6

CCCCAGCCACATGAGCGAGGACTGCTTCTGGAAGATATACTTCGTACTGCTGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAGTTACAAGGCAGCCACGGCGACACCGTACCTGTGGCTCTCGGCGATGAAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 6

CCCCAGCCACATGAGCGAGGACTGCTTCTGGAAGATATACTTCGTACTGCTGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAGTTACAAGGCAGCCACGGCGACACCGTACCTGTGGCTCTCGGCGATGAAG


Block sizes: 22 (upstream exon), 44 (downstream exon)
Score: 5

CCCCAGCCACATGAGCGAGGACTGCTTCTGGAAGATATACTTCGTACTGCTGCATCCTAAGCTCAGGAAGGATGATGCCGACATTTTATCCACTCCACAGgtgattttcc ... cttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAGTTACAAGGCAGCCACGGCGACACCGTACCTGTGGCTCTCGGCGATGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagacattgtttgctagcagacgattcttatcggttcctgattgccttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAGTTACAAGGCAGCCACGGCGACACCGTACCTGTGGCTCTCGGCGATGAAG
                                         ttgcctt  CT-rich tract
                       attcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgcacacaaaaaaaaaaaaagataagccactatctgccagctcaagacattgtttgctagcagacgattcttatcggttcctgattgccttgatacagATTCTGGAAGCTAGGGACAAGTTGTCGCAGGAGGTGCGGTACCGGACGGAGTTACAAGGCAGCCACGGCGACACCGTACCTGTGGCTCTCGGCGATGAAG

actgcac
- - - - caaaaaa
- - - - -aaaaaaa
- - - - - - - - - - - - - -gccacta
- - - - - - - - - - - - - - - - - - tgccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc