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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctgagctctatcattcaagggtgtctaagcatgtcatatcatctgcatcctttctgttctcatttaaatgtgctaaatttatttccttataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAGGAGGCAAAGCAACAGATACTAAAAATCCAGATGGTGTTGGTGCAGGACG

Basic information

species Zea mays
transcript GRMZM2G015902_T01
intron # 5
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|71332981|gb|DR803517.1|DR803517
EST:     GCTGATTATTTCC-CCGT-GCAAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: GCTGATTATTTCCACCGTGGC-AAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|76935876|gb|DV174501.1|DV174501
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAAAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCC
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCC
EST: gi|211001835|gb|FL114781.1|FL114781
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|149014683|gb|EE044352.2|EE044352
EST:     GCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCC
genomic: GCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGA-Ggtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCC
EST: gi|211001836|gb|FL114782.1|FL114782
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAGAAATTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|211001838|gb|FL114784.1|FL114784
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAGAAATTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|71332986|gb|DR803518.1|DR803518
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|76018908|gb|DT946078.1|DT946078
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGG
EST: gi|20802771|gb|BQ293821.1|BQ293821
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|211001837|gb|FL114783.1|FL114783
EST:     GGCTGATTATTTCCACCGTGGCAAAGAATATGATGAGAAATTGCGAAGAG                         AGAATTCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCA
genomic: G-CTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAAT-CCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCA
EST: gi|211001833|gb|FL114779.1|FL114779
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAGAAATTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|78116755|gb|DV535142.1|DV535142
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|91870478|gb|EB400898.1|EB400898
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGCGTTGTACAAAGATAATGATTCTCGGCCCAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|148960852|gb|EE011528.2|EE011528
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGAAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|71446263|gb|DR827313.1|DR827313
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGGCAAGTGGAAATCCA
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCA
EST: gi|211001832|gb|FL114778.1|FL114778
EST:     TGCTGATTATTTCCACCGKGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|71770078|gb|DR968015.1|DR968015
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAG
EST: gi|71323571|gb|DR798454.1|DR798454
EST:     TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAG                         AGAATCCTGGGTTGTACAAAGATAATGA
genomic: TGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGA

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), 47 (downstream exon)
Score: 67

AGGCTTGCAAGAAAACCAAAACCAGATGCAAACATTCCATCAAGTTATAGTGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAGGAGGCAAAGCAACAGATACTAAAAATCCAGATGGTGTTGGTGCAGGACG


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

AGGCTTGCAAGAAAACCAAAACCAGATGCAAACATTCCATCAAGTTATAGTGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAGGAGGCAAAGCAACAGATACTAAAAATCCAGATGGTGTTGGTGCAGGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

AGGCTTGCAAGAAAACCAAAACCAGATGCAAACATTCCATCAAGTTATAGTGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAGGAGGCAAAGCAACAGATACTAAAAATCCAGATGGTGTTGGTGCAGGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 41

AGGCTTGCAAGAAAACCAAAACCAGATGCAAACATTCCATCAAGTTATAGTGCTGATTATTTCCACCGTGGCAAAGAATATGATGAAAAACTGCGAAGAGgtttgttacc ... tataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAGGAGGCAAAGCAACAGATACTAAAAATCCAGATGGTGTTGGTGCAGGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatcctttctgttctcatttaaatgtgctaaatttatttccttataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAGGAGGCAAAGCAACAGATACTAAAAATCCAGATGGTGTTGGTGCAGGACG
                            tgctaaa  putative branch site (score: 41)
                                   tttatttcctt  CT-rich tract
                   atttaaatgtgctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctgagctctatcattcaagggtgtctaagcatgtcatatcatctgcatcctttctgttctcatttaaatgtgctaaatttatttccttataatgcagAGAATCCTGGGTTGTACAAAGATAATGATTCTCGGCCAAGTGGAAATCCAGGAGGCAAAGCAACAGATACTAAAAATCCAGATGGTGTTGGTGCAGGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
tttctga
- - - - - - - cattcaa
- - - - - - - - - - - - - - -aagcatg
- - - - - - - - - - - - - - - - - - - - - catctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgcta