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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatcaaactcctatctttcaatcatctttttttcttctcggacgcgcaagagatatgcacatcattaaattaagaagaagtttggtccaaaata...

Basic information

species Zea mays
transcript GRMZM2G574782_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g29370.1 (Oryza sativa), 5'ss of exon 4
CAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatcaaactcctatctttcaatc---atctttttttcttctcggacgcgcaagagatatgcacatcattaaattaagaagaagtttggtccaaaata
 |||||||| ||||| ||||| |||| ||| ||||||||  ||||||| |||||||| || |||||||||||||||||||||||||| ||   |||||||||||| ||  |   ||||   ||  | |     | | |   ||||| |  |    |||    |||     |  |    |        |  || ||    |   
TAAAGGAATTAAAGGCCATGGTTACCGTGACGAATTGGTGGTTCCTATAATTGAGAACACTCCTTATGAGTATGAGCTCACTGACTCACTGGCTGAGGCGgtatgttactattgtccttctttggagtttcagtttctcaatcttcgcaaaaaaacaaatattatatttgtagtctgttgttctcataacttcgtgtgga---
















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|76289240|gb|DV028808.1|DV028808
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|211266802|gb|FK955969.1|FK955969
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAAC-ACGGAAT-
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|21809578|gb|BQ667896.1|BQ667896
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTG
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTG
EST: gi|32862805|gb|CF002487.1|CF002487
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|148939493|gb|EC884073.2|EC884073
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|148956120|gb|EC901887.2|EC901887
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|31359134|gb|CD443491.1|CD443491
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|20507404|gb|BQ279616.1|BQ279616
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGC
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGC
EST: gi|148939957|gb|EC884685.2|EC884685
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGGATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|60351211|gb|DN218184.1|DN218184
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|91876905|gb|EB406862.1|EB406862
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAAT
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCC-AAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAAT
EST: gi|26456641|gb|CA828224.1|CA828224
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACT
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACT
EST: gi|148957566|gb|EC903663.2|EC903663
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|31355926|gb|CD440283.1|CD440283
EST:     CCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: CCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|12967932|gb|BG264879.1|BG264879
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|149079628|gb|EE168621.2|EE168621
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGGACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|149079514|gb|EE168492.2|EE168492
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATA
EST: gi|109179163|gb|EC379844.1|EC379844
EST:     TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCG                         ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGCAAT
genomic: TTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGG-AAT

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: 371

CAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 560

CAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 799

CAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 232

CAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatc ... tatttatcagATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCACTGACTCCCTAAGTGAGGCGgtatgctatcaaactcctatctttcaatcatctttttttcttctcggacgcgcaagagatatgcacatcattaaattaagaagaagtttggtccaaaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaagaa