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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatgtcgccatttagtgtgttgatgtatgtttgttgagtgtttaatttcgttgtcttctgttgctgcag

Basic information

species Zea mays
transcript GRMZM2G035150_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g64219.1 (Oryza sativa), 5'ss of exon 9
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatgtcgcc-atttagtgtgttgatgta----tgtttgttgagtgt-ttaatttcgttgtcttctgttgc-----tgcag-----
|||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||    ||||    |  ||  ||||| || ||    ||| | ||  | |  || ||   || |    |   |||     ||  |     
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttgtcatttagataccgtgttcatctaggagtgtctctttggcggattgatgcggtagctcaccagtgcatgtttgtggtgcag

upper sequence: GRMZM2G035150_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g64219.3 (Oryza sativa), 5'ss of exon 7
-------------------------------------------TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatgtcgcc-atttagtgtgttgatgta----tgtttgttgagtgt-ttaatttcgttgtcttctgttgc-----tgcag-----
                                           |||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||    ||||    |  ||  ||||| || ||    ||| | ||  | |  || ||   || |    |   |||     ||  |     
GTATCTAATGTGTTTCTGTTCATTTTTTCCTTAAAAAACCCAGTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttgtcatttagataccgtgttcatctaggagtgtctctttggcggattgatgcggtagctcaccagtgcatgtttgtggtgcag

upper sequence: GRMZM2G035150_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g39230.1 (Oryza sativa), 5'ss of exon 16
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatgtcgccatt-tagtgtgttgatgtatgtttgttgagtgtttaatttcgttgtcttctgttgctgcag----------------------
  |||||| | |||||||||||||||||||||||| | ||  ||||| | |||  ||||||    |||||   |  ||  |||||  | || |  |  | ||| | |  ||| |  |  |  || ||  ||                        
AGATATGCATTAGTTTTTGGGCTGAGGTGCACTACGATTCGGTATATGCAGAAAAAGgtacagtttgtcgttttgatacagtgttcttctaggagtact-agtatctc-tttggcaggttgatgctgtagctcatgtgtgcaagttgtggtgcag

upper sequence: GRMZM2G035150_T03 (Zea mays), 5'ss of exon 10
lower sequence: EFJ31563 (Selaginella moellendorffii), 5'ss of exon 8
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatgtcgccatttagtgtgttgatgtatgtttgttgagtgtttaatttcgttgtcttctgttgctgcag
| |||| ||| || ||||||||||| ||||||||||||||| | ||||| ||||||||||       | |   | |       || | | || |  |  |    |   | |||  |                
TCATATTCTTAAGCTTTTGGGCTGAAGTGCACTACAACTCCGTGTATCCGGAAGGAGgta-------tagttttgtgaaacactggtatgtgctc-tcaaccact--gtgtcgcag----------------

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|74235678|gb|DT643592.1|DT643592
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|78092883|gb|DV521257.1|DV521257
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|4804174|gb|AI666040.1|AI666040
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|32808275|gb|CD960509.1|CD960509
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|76289426|gb|DV028994.1|DV028994
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|71427953|gb|DR809003.1|DR809003
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|32793686|gb|CD945922.1|CD945922
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|86466720|gb|DY233090.1|DY233090
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|71427180|gb|DR808230.1|DR808230
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|50324081|gb|CO519207.1|CO519207
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|50331811|gb|CO526937.1|CO526937
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTTT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|78080763|gb|DV509175.1|DV509175
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|24462661|gb|BM660192.1|BM660192
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGTCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
EST: gi|50327716|gb|CO522842.1|CO522842
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG                         AGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCT

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: 45 (upstream exon), 45 (downstream exon)
Score: 62

TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCTAGCTAGGATTCCCAGGACAGACTAGATAGAGCAGCTTTAACAGACTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCTAGCTAGGATTCCCAGGACAGACTAGATAGAGCAGCTTTAACAGACTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCTAGCTAGGATTCCCAGGACAGACTAGATAGAGCAGCTTTAACAGACTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatg ... gttgctgcagAGTTGCCGGTTTTGGAGTTTGACAACAAAAGGAAAAGGTGGTGGCCCTTCTAGCTAGGATTCCCAGGACAGACTAGATAGAGCAGCTTTAACAGACTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatgtcgccatttagtgtgttgatgtatgtttgttgagtgtttaatttcgttgtcttctgttgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG