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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcaggtgtctgaaaggaattccaattttatacctaatattctgccagaataagtagctagttcattccagtggcaataaatgtgttgacctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCC

Basic information

species Zea mays
transcript GRMZM2G574782_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 1
atgcaggtgtctgaaaggaat--tccaattttatacctaatattctgccagaat--aagtagctagttcattcc-----agtggcaataaatgtgttgacctc--tttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCC
            ||| |  ||  || |    |  |||  |  |||||  || |   | || || | || |  |      |  |  |  | |  | || | | |  | |||||||||||||||||||||||||| |||||||||||||||||| || | ||||||||||| ||||| ||  | |||||| ||||||||||||||||||||||
-----------agaacgtgattttctaccagtcgaccataacttctgtgagcactaaggttgcgatttgaaccaaaagaaacgatataagaaattttaatcacattctcagGTGTGCAGAAGGAGAGGATGGTGGCAGAGGACATGTATGTGCTGTCAGCAGATGGGAAGGTGCTCTCCTCACCTGTATCAAAGCCATGGCCAAACAAGCC
















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|148973039|gb|EE024097.2|EE024097
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|76289240|gb|DV028808.1|DV028808
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|211266802|gb|FK955969.1|FK955969
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|211264368|gb|FK955956.1|FK955956
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCTTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|21809578|gb|BQ667896.1|BQ667896
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|211266798|gb|FK955965.1|FK955965
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCTTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|148938308|gb|EC882615.2|EC882615
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|211266801|gb|FK955968.1|FK955968
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCTTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|148939493|gb|EC884073.2|EC884073
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|211266800|gb|FK955967.1|FK955967
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCTTCCG                         GTGTGCAGAAGGAGAGGATGGTA
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTA
EST: gi|148956120|gb|EC901887.2|EC901887
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|31359134|gb|CD443491.1|CD443491
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|20507404|gb|BQ279616.1|BQ279616
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTTATCTTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|148939957|gb|EC884685.2|EC884685
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|91876905|gb|EB406862.1|EB406862
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|26456641|gb|CA828224.1|CA828224
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|148957566|gb|EC903663.2|EC903663
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|211264372|gb|FK955960.1|FK955960
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTGGGCTTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|149079628|gb|EE168621.2|EE168621
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|149079514|gb|EE168492.2|EE168492
EST:     CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
EST: gi|211266805|gb|FK955972.1|FK955972
EST:     CGACCCCGCCGTGCCGCTCGCCGACCGCCTCATCGTTATGTCACCTTCCG                         GTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG
genomic: CGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 494

GCGCAGGGATGGGTCACGGGCACCGGCGGCAGCATCACCGTCAAGGTCAACGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 771

GCGCAGGGATGGGTCACGGGCACCGGCGGCAGCATCACCGTCAAGGTCAACGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 732

GCGCAGGGATGGGTCACGGGCACCGGCGGCAGCATCACCGTCAAGGTCAACGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 289

GCGCAGGGATGGGTCACGGGCACCGGCGGCAGCATCACCGTCAAGGTCAACGACCCCACCGTGCCGCTCGCCGATCGCCTCATCGTTATGTCACCCTCCGgtaaccagcg ... cctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagaataagtagctagttcattccagtggcaataaatgtgttgacctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCC
                                       tgttgac  putative branch site (score: 289)
                                             cctctttc  CT-rich tract
                               aataaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcaggtgtctgaaaggaattccaattttatacctaatattctgccagaataagtagctagttcattccagtggcaataaatgtgttgacctctttcagGTGTGCAGAAGGAGAGGATGGTAGCAGAGGACATGTATGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- gcaggtg
- - - - - - gaaaggaa
- - - - - - - - - - - - - - - - - - - - ttctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttg