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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGTGCAGAGAAAGGATCAGGAGTATCTGTGAATCTTGACTGGAAGATTGGGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgcgaattgctgtaccgagctacagttctaaatgtcatgagctcaagttcaatgcaatatttggtgtttgttaattgaataccgcctctcttttgtgcag

Basic information

species Zea mays
transcript GRMZM2G414569_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G414569_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 2
TAGTGCAGAGAAAGGATCAGGAGTATCTGTGAATCTTGACTGGAAGATTGGGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgcgaattgctgtaccgagctacagttc---taaatgtcatgagctcaagttcaatgcaatatttggtgtttgttaattgaataccgcctc-tcttttgtgcag
||| ||||||||||| |||||| ||||| | |||||||| ||||||||||| || ||| |||| |||||||||| ||| ||||||||||||||||||||||| ||  |  |  | ||   || |    || || |   | |   |  |   || | || || |  |||  |   || || |  | |   | |   ||  |   || || ||
TAGCGCAGAGAAAGGGTCAGGAATATCTATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgc-tgacggtccatatgaccatatttcactgatgtccagtttaat--tcactgcttctctaattgctgcaatctaattccttttgtag
















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|5846833|gb|AI999916.1|AI999916
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|60352391|gb|DN219364.1|DN219364
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTACAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|71450228|gb|DR831278.1|DR831278
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|18179418|gb|BM380628.1|BM380628
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|91869882|gb|EB400589.1|EB400589
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|5770138|gb|AI973312.1|AI973312
EST:     GGATCGCANCAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|60394039|gb|DN226909.1|DN226909
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTACAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|91869884|gb|EB400590.1|EB400590
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|5325020|gb|AI783211.1|AI783211
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|211528538|gb|FL329337.1|FL329337
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|40286941|gb|CK327333.1|CK327333
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTACAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|18174124|gb|BM349512.1|BM349512
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|6020792|gb|AW065720.1|AW065720
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCAT
EST: gi|6020682|gb|AW065490.1|AW065490
EST:     GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCC
genomic: GGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCC

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: 43 (upstream exon), 46 (downstream exon)
Score: 49

TAGTGCAGAGAAAGGATCAGGAGTATCTGTGAATCTTGACTGGAAGATTGGGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCATCAGAACTTGATATACCTCAAAGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 54

TAGTGCAGAGAAAGGATCAGGAGTATCTGTGAATCTTGACTGGAAGATTGGGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCATCAGAACTTGATATACCTCAAAGAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 86

TAGTGCAGAGAAAGGATCAGGAGTATCTGTGAATCTTGACTGGAAGATTGGGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCATCAGAACTTGATATACCTCAAAGAAAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 63

TAGTGCAGAGAAAGGATCAGGAGTATCTGTGAATCTTGACTGGAAGATTGGGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgc ... ttttgtgcagGGTGTAGAACTAGAGCTTCGGAAACTTGAAGTGGCAGTGCAGGCCATTCATCAGAACTTGATATACCTCAAAGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGTGCAGAGAAAGGATCAGGAGTATCTGTGAATCTTGACTGGAAGATTGGGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgcgaattgctgtaccgagctacagttctaaatgtcatgagctcaagttcaatgcaatatttggtgtttgttaattgaataccgcctctcttttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA