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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagcttgtacttagtttttgcttgttttctttattgattgtttgaggttaacaaagtccccccccccccaaccaccaaatgcctgcag

Basic information

species Zea mays
transcript GRMZM2G008556_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 3
CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagcttgtacttagtttttgcttgttttctttattgattgtttgaggttaacaaagtccccccccccccaaccaccaaa-tgcctgcag
||||||||||| ||||||||||||  ||||||||||||| |||||||||| ||||| || ||||||||||   | ||| || || || |||   ||| | | || |    ||||| || | |      ||    |     |||  |  |||     |||||
CTTACAGATGAGTTGGAGAAGATGTTTGAGAAACTCAAGTTGACAGAATCACTCCTTGACAGCAAAgtat-gtatcttataatttgtgtttatctgtatccgttgtct-ctgttttagctga------tcttttctttaacaatgataaaaacaaatgcag
















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|149070070|gb|EE158471.2|EE158471
EST:     AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAA                         AATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
genomic: AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
EST: gi|78082127|gb|DV510539.1|DV510539
EST:     AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGNAAGCAAA                         AATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
genomic: AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
EST: gi|71426785|gb|DR807835.1|DR807835
EST:     AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAA                         AATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
genomic: AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
EST: gi|26456440|gb|CA828023.1|CA828023
EST:     GAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAA                         AATCTTGAAGTTAAAAAGATAAACGATGAGAAAAAAGCTGCATTGGCTGCC
genomic: GAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
EST: gi|149109119|gb|EE190019.2|EE190019
EST:     AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAA                         AATCTTGAAGTTTAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
genomic: AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
EST: gi|20803029|gb|BQ294079.1|BQ294079
EST:     CTCTCCTCGAAAGCAAA                         AATCTTGAAGTTAAAAAGATAAACGATGAGAAAAAAGCTGCATTGGCTGCC
genomic: CTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
EST: gi|71448531|gb|DR829581.1|DR829581
EST:     AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAA                         AATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC
genomic: AGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCC

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: 144

CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCCCAGTTTGCAGCAGAAGCAACTTTGCGAAGAGTACATGCAGCCCAGAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 72

CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCCCAGTTTGCAGCAGAAGCAACTTTGCGAAGAGTACATGCAGCCCAGAAAG


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

CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCCCAGTTTGCAGCAGAAGCAACTTTGCGAAGAGTACATGCAGCCCAGAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 78

CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagc ... atgcctgcagAATCTTGAAGTTAAAAAGATAAATGATGAGAAAAAAGCTGCATTGGCTGCCCAGTTTGCAGCAGAAGCAACTTTGCGAAGAGTACATGCAGCCCAGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTCGAAAGCAAAgtatcacagcttgtacttagtttttgcttgttttctttattgattgtttgaggttaacaaagtccccccccccccaaccaccaaatgcctgcag

- - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA