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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtcttattcacatgtttgatgcatacacttccatactcgtacccaagtgtccaactaatttaatcgtacttttgacttaag

Basic information

species Zea mays
transcript GRMZM2G375904_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 9
TGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtcttattcacatgtttgatgcatacacttccatactcgtacccaagtgtccaactaatttaatcgtacttttgacttaag
|||||||||||||||| ||||||||||||||| |||||||||||| ||| | ||||||||||||||  ||||||| ||||||||||||||||| ||||||||||| |||  |  | ||||   ||       |||   | |||  | |   |||   || || | |  || ||   |  |||| ||
TGAAGAGGCAAAGCTTTCTCCTGAAGCTAAGGATCTCATCAGCAAACTTCTATGTAATGTTGAGCAGAGACTTGGAACAAAAGGAGCCCATGAGATAAAAgtgcgctctcttctatatgtacaatat-----ctttattgctctcaactgtgtgcttaattattatcgtcatatgctctactttag
















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|5895617|gb|AW036863.1|AW036863
EST:     TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
genomic: TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
EST: gi|28187719|gb|CB179329.1|CB179329
EST:     TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
genomic: TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
EST: gi|5901099|gb|AW042199.1|AW042199
EST:     TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGATATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
genomic: TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
EST: gi|33285627|gb|CF075422.1|CF075422
EST:     TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCGGATGAAA
genomic: TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
EST: gi|211195854|gb|FL001022.1|FL001022
EST:     CGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
genomic: TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
EST: gi|31628455|gb|CD526616.1|CD526616
EST:     TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCGGATGAAA
genomic: TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
EST: gi|149049839|gb|EE048526.2|EE048526
EST:     TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
genomic: TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
EST: gi|32870336|gb|CF010018.1|CF010018
EST:     TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
genomic: TGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
EST: gi|32928081|gb|CF032893.1|CF032893
EST:     ACAAAAGGAGCCCATGAAATAAAA                         GCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA
genomic: ACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAA

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), 49 (downstream exon)
Score: 55

TGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

TGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

TGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

TGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtctt ... ttgacttaagGCGCATCCATGGTTCGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAGGCAAAGCTTCCTCCTGAAGCTAAGGCTCTCATCAGCAAGCTTTTGTGTAATGTTGAGCATCGACTTGGTACAAAAGGAGCCCATGAAATAAAAgtgcggtcttattcacatgtttgatgcatacacttccatactcgtacccaagtgtccaactaatttaatcgtacttttgacttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG