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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACCCCTGCATGACCCGATTGCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatattttccttgtttgtttttttgcaaaatactctctctgtcctaaatacaagggtcaaacaattttaggactaaataaggagtctgacaaaaga...

Basic information

species Zea mays
transcript GRMZM2G111014_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111014_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 10
AAACCCCTGCATGACCCGATTGCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaa--tattttccttgtttgtttttttgcaaaatactctctctgtcctaaatacaagggtcaaacaattttaggactaaataaggagtctgacaaaaga--
||| |||| ||||| || || || |||||||| ||  ||||||| |||||||||||||| |||||||||||||||||  || || | | | |||  |||||| || | |         |   || | | |   |||     |    || ||   |    | ||||  |   |   
AAATCCCTTCATGATCCAATCGCATTCAGAAAAGAAATGGATGGAATAACAGTGGATGTTTCCCTTCAATGgtaaaatgtacttccttggcttgaatttttgaaagaaaaagaa---ataaaaagtcctaatatcatgtcctccatggtctgtttggtca-tctgctagctggta
















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|211423929|gb|FL064832.1|FL064832
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32925384|gb|CF030196.1|CF030196
EST:     GCGTTCAGAAAGGAGTTGAATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32925421|gb|CF030233.1|CF030233
EST:     GCGTTCAGAAAGGAGTTGAATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32925143|gb|CF029955.1|CF029955
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32925179|gb|CF029991.1|CF029991
EST:     GCGTTCAGAAAGGAGTTGAATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32924802|gb|CF029614.1|CF029614
EST:     GCGTTCAGAAAGCCCTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32924772|gb|CF029584.1|CF029584
EST:     GCGTTCAGAAAGGAGTTGAATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTTGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32926646|gb|CF031458.1|CF031458
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|211423925|gb|FL064828.1|FL064828
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32926818|gb|CF031630.1|CF031630
EST:     GCGTTCAGAAAGGAGTTGAATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32926591|gb|CF031403.1|CF031403
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32925737|gb|CF030549.1|CF030549
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32925461|gb|CF030273.1|CF030273
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32925062|gb|CF029874.1|CF029874
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|211426532|gb|FL064833.1|FL064833
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32926568|gb|CF031380.1|CF031380
EST:     GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
EST: gi|32925900|gb|CF030712.1|CF030712
EST:     GCGTTCAGAAAGGAGTTGAATGGTATAACAGTGGATGTCTCCCTTCAATG                         GTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG
genomic: GCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCG

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: 278

AAACCCCTGCATGACCCGATTGCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCGCACTATTGATGGTGGTACTCATATTGATGGTCTAAAGGCTTCATTGACG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 102

AAACCCCTGCATGACCCGATTGCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCGCACTATTGATGGTGGTACTCATATTGATGGTCTAAAGGCTTCATTGACG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 46

AAACCCCTGCATGACCCGATTGCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCGCACTATTGATGGTGGTACTCATATTGATGGTCTAAAGGCTTCATTGACG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 60

AAACCCCTGCATGACCCGATTGCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatatt ... ccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCGCACTATTGATGGTGGTACTCATATTGATGGTCTAAAGGCTTCATTGACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACCCCTGCATGACCCGATTGCGTTCAGAAAGGAGTTGGATGGTATAACAGTGGATGTCTCCCTTCAATGgtaaaatattttccttgtttgtttttttgcaaaatactctctctgtcctaaatacaagggtcaaacaattttaggactaaataaggagtctgacaaaaga

- - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaaag