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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgatggtttcacatccacatcctttccatccttgcccattgtgctaaagaaagtttacaacttcgagaaaaatctggtcggttatgttatcttgattgagctttcttattttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA

Basic information

species Zea mays
transcript GRMZM2G002859_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 7
gt-ctgatggtttcacatccacatcctttccatccttgcccattgtgctaaagaaagtttacaact-tcgagaaaaatctggtcggttatg-ttatcttgattgagctttcttattttttttct-----agATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTC---CGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA
|| |||||| |||   | |  |||||||  ||  |||   ||       |||| || ||   |||| |||| ||| | ||| |  ||| || ||||| ||||| || | |||| ||| ||| ||     ||||||||||||||||||||||||| |||||||||||||   | |  ||||||||||| ||||| ||||| ||| ||||||||||| | || ||| | ||||   
gtactgatgattttgta-cagcatccttatcaaacttatacaga-----aaaggaacttgttaactatcgaaaaagaactgctttgttttggttatcctgattcag-tctcttgtttctttacttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAGAGTTCTATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCA---
















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|71307047|gb|DR789678.1|DR789678
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|149070323|gb|EE158722.2|EE158722
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATTTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|33091909|gb|CF051903.1|CF051903
EST:     GAAATTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|148986436|gb|EE030178.2|EE030178
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATTTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|40336986|gb|CK371056.1|CK371056
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|40335185|gb|CK369255.1|CK369255
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|60356623|gb|DN223596.1|DN223596
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|37380473|gb|CF627052.1|CF627052
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT

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: 349

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 135

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaaaatctggtcggttatgttatcttgattgagctttcttattttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA
                        tcttgat  putative branch site (score: 195)
                                   ctttcttatttttttt  putative PPT
                                    tttcttattttttttc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgatggtttcacatccacatcctttccatccttgcccattgtgctaaagaaagtttacaacttcgagaaaaatctggtcggttatgttatcttgattgagctttcttattttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT