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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaccacaaatgctgaaatgcacatattattctgttgatatttttttcttgacatctataaccaatactcctttttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC

Basic information

species Zea mays
transcript GRMZM2G085577_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 3
gtatgaaccacaaatgctgaaatgcacatattattctgttgatatttttttcttgacatctataaccaatactcctttttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC
|||  |||    ||||   | | |  | | |       |   | || | |   ||      || | | | | |  || |||  ||||||| |||||||| ||||| |||  |||||||||  | || | |||  |||||||||||||||| |||||||||||||| ||||| ||
gtaccaactg-gaatgtacacaagttcctctctcgtcatcagt-ttctctagctgctgctgatgagccaca-tgtttatttctttcagAAGTTCAGCCCATGGGAAATTGTCAGGCATGACATTGTATACCCAATCAGATTTTTTGGCCACGTTGAGATTTTGCCAGATGGATC

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgaaccacaaatgctgaaatgcacatattattctgttgatatttttttcttgacatctataaccaatactcctttttt-----tcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC
         |  | ||      ||   || | |   | | |       |||  ||| | || ||||  || |||  ||  |     | | |||||||||||||| ||||| |||   ||||| || ||||| ||||||||||||||||| ||| | ||  |  |    || ||||| ||
------gtgatgattgtcagtgtggtgatttcaacttatgg-------ttttctgagaactgtaactcatcctctattaatgggaatttgcagAAATTCAGCCCATGGGAAATTGTGAGGCACGACGTGGTATTCCCTGTCAGATTTTTCGGCAAGGTGCAAGTAAATCCGGATGGATC
















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|148961830|gb|EE012612.2|EE012612
EST:     AACACATTGCCAAGGAGGGCCAGGAAGAAGTTGCAGAAGATTGGCTTGAT                         AAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGA
genomic: AACACATTGCCAAGGAGGGCCAGGAAGAAGTTGCAGAAGATTGGCTTGATgtatgaacca ... ttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGA
EST: gi|87155862|gb|DY400651.1|DY400651
EST:     CACATTGCCAAGGAGGGCCAGGAAGAAGTTGCAGAAGATTGGCTTGAT                         AAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGA
genomic: CACATTGCCAAGGAGGGCCAGGAAGAAGTTGCAGAAGATTGGCTTGATgtatgaacca ... ttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGA
EST: gi|22133496|gb|BQ833744.1|BQ833744
EST:     AGTTGCAGAAGATTGGCTTGAT                         AAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGG-GTTCCCTGTCAGA
genomic: AGTTGCAGAAGATTGGCTTGATgtatgaacca ... ttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGA
EST: gi|26558458|gb|CA830693.1|CA830693
EST:     AGAAGATTGGCTTGAT                         AAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGG-GTTCCCTGTCAGA
genomic: AGAAGATTGGCTTGATgtatgaacca ... ttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGA

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: 379

TTTGCCTGCTTGGGGCTATGGCCTGCGTTACCGATATGGACTGTTCAAACAACACATTGCCAAGGAGGGCCAGGAAGAAGTTGCAGAAGATTGGCTTGATgtatgaacca ... ttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

TTTGCCTGCTTGGGGCTATGGCCTGCGTTACCGATATGGACTGTTCAAACAACACATTGCCAAGGAGGGCCAGGAAGAAGTTGCAGAAGATTGGCTTGATgtatgaacca ... ttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 95

TTTGCCTGCTTGGGGCTATGGCCTGCGTTACCGATATGGACTGTTCAAACAACACATTGCCAAGGAGGGCCAGGAAGAAGTTGCAGAAGATTGGCTTGATgtatgaacca ... ttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 502

TTTGCCTGCTTGGGGCTATGGCCTGCGTTACCGATATGGACTGTTCAAACAACACATTGCCAAGGAGGGCCAGGAAGAAGTTGCAGAAGATTGGCTTGATgtatgaacca ... ttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttgatatttttttcttgacatctataaccaatactcctttttttcttcagAAATTCAGCCCTTGGGAGATTCCCAGGCATGATGTGGTGTTCCCTGTCAGATTTTTTGGCCATGTTGAGATTTTGCCTGATGGCTC
                          ctataac  putative branch site (score: 502)
                                ccaatactcctttttt  CT-rich tract
     ttgatatttttttctt  TA-rich tract