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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatatctttgcctattgcctactattttagtcaaatagcactgtttcattggaaaattcataaaatgcaatagtattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT

Basic information

species Zea mays
transcript GRMZM2G701689_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g41230.2 (Oryza sativa), 3'ss of exon 4
gtactatatctttgcctattgcctactattttagtcaaatagcactgtttcattggaaaattcataaaatgcaatagtattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT
||||| | | | |      |||| | |||| |||   |  || ||  ||||  |||  || |||| |||  ||||| |  | ||||| || ||||| || | |||||||||||| || |||||||||||||| ||||||||||| |||||| |||| ||
gtactttgtttcta-----tgcccattattataggtcatgagaaccatttcgctgggcaaatcatgaaacacaataatgctatgcagACACAAGTTCGACAATGGTGATGGCACGTCGTGCAAGCGTTGTAGCTGTAAGAAGTCAAAATGCTTGAAGCT
















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|31359966|gb|CD444323.1|CD444323
EST:     GATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAG                         GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
genomic: GATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
EST: gi|31349638|gb|CD433995.1|CD433995
EST:     GATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAG                         GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
genomic: GATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
EST: gi|32932451|gb|CF037263.1|CF037263
EST:     CAAGAAGAAAAG                         GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
genomic: CAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
EST: gi|19351600|gb|BM896132.1|BM896132
EST:     TGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAG                         GCATAAGTTTGATAGTGGTGATGGCACTTCATGCA-GCGTTGTAGTTGTAA
genomic: TGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
EST: gi|31357841|gb|CD442198.1|CD442198
EST:     GATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAG                         GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
genomic: GATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
EST: gi|19351662|gb|BM896194.1|BM896194
EST:     GATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAG                         GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
genomic: GATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
EST: gi|76915167|gb|DV165860.1|DV165860
EST:     CGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAG                         GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA
genomic: CGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAA

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: 257

CGGCACCTTCTGAGCAAAACATTATAAATGATGATTTCACTCAAACAACTGATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

CGGCACCTTCTGAGCAAAACATTATAAATGATGATTTCACTCAAACAACTGATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 318

CGGCACCTTCTGAGCAAAACATTATAAATGATGATTTCACTCAAACAACTGATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 176

CGGCACCTTCTGAGCAAAACATTATAAATGATGATTTCACTCAAACAACTGATGTTGCAACCGCTGAAGCTTCTAGTCAGGGTAGTCCCAAGAAGAAAAGgtactatatc ... tattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcaaatagcactgtttcattggaaaattcataaaatgcaatagtattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT
                        aaaattcataaaatgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatatctttgcctattgcctactattttagtcaaatagcactgtttcattggaaaattcataaaatgcaatagtattttgcagGCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT