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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgctcttattctaatttcgctaattcttagtgatataaataatttctgttgacaacaccacgtagtggaagagattgctcatgatacaaaactt...

Basic information

species Zea mays
transcript GRMZM2G000393_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g07905.2 (Oryza sativa), 5'ss of exon 4
---TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgctcttattctaatt-tcgctaattcttagtgatataaataatttctgttgacaacaccacgtagtggaagagatt--gctcatgatacaaaactt--------------------------------------------------------------------------------
   || ||||||||| |||   | ||||| || ||||||||||||||||| ||||| ||||| ||||||||||||  |||||||||||| |||||||| ||||||| |||| ||||  |||  |  |  | | ||    | |||| ||    |      ||| ||||    || |      || ||    |  |  |  || |  |                                                                                
AGTTCTGACAAGAAGAAGC---TCCTTGCTGTTATTGGAGTTTACACTGGTTTTGGTTCCCGGCTCAAGAGGAACACCTTCCGTGGCTCATGGATGCCGAGAGgttcgctgttcttgctcttttagtttccagtttacggcgataaaatgtgtgcgccctgataacatttggttggaatgcagcttcatttttttttctaatagctattgctgatgcaaactatgttacttataaggtttcaactacaggagtataattgttcttttacctcactgtaaatttcag
















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|6626361|gb|AW257893.1|AW257893
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GNGATGCTCTGAAGAAGCTTGAGGAAAAG
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAG
EST: gi|211507519|gb|FL321825.1|FL321825
EST:     GGCTCCCGTCTCAAGAG-AACGTCTTCCCGTG-CTC-TGNATGCAAAGAG                         -TGATGCTCTGAA
genomic: GGCTCCCGTCTCAAGAGGAACGTCTTCC-GTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAA
EST: gi|21843330|gb|BQ703911.1|BQ703911
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|78090931|gb|DV519305.1|DV519305
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAA-GGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|211340421|gb|FL351902.1|FL351902
EST:     GGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCCTGGATGC-AAGAG                         GTGATGCTCTGAAGAAGC
genomic: GGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCC-TGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGC
EST: gi|76015038|gb|DT942208.1|DT942208
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|22819731|gb|BU499821.1|BU499821
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|4621544|gb|AI612377.1|AI612377
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA
EST: gi|149084753|gb|EE174248.2|EE174248
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGA
EST: gi|71448461|gb|DR829511.1|DR829511
EST:     TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAG                         GTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCCTTTTGTTA
genomic: TGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTA

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: 136

TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTATTGGTCGGAGGTTTTGTTCTGGATCTATACCTTTGAGTTACTGCATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTATTGGTCGGAGGTTTTGTTCTGGATCTATACCTTTGAGTTACTGCATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTATTGGTCGGAGGTTTTGTTCTGGATCTATACCTTTGAGTTACTGCATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgct ... taaattgcagGTGATGCTCTGAAGAAGCTTGAGGAAAAGGGTGTAGCTATTCGTTTTGTTATTGGTCGGAGGTTTTGTTCTGGATCTATACCTTTGAGTTACTGCATCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGACAAGAAGCAGCAGCTTCTTGCCGTCATTGGAGTTTACACTGGGTTTGGCTCCCGTCTCAAGAGGAACGTCTTCCGTGGCTCCTGGATGCCAAGAGgtttgctgctcttattctaatttcgctaattcttagtgatataaataatttctgttgacaacaccacgtagtggaagagattgctcatgatacaaaactt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA