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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagtgttttgtgtttaggtgatatttaagtgttctcctagtctcctttgtttcttatgcacgtccttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 5
gtaagagtgttttgtgttt---aggtgatatttaagtgttctcctagtctcctttgtttcttatgcacgtccttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG
||| |||| | |||| |||   ||||||  ||||||   | || |       ||||   || |||    ||  | |  ||||||||||||||||||| |||||| ||||||| ||||| || ||||| ||| ||||||| |||||||| || ||||||||||| ||||||||||| |||||
gta-gagtctcttgtattttgaaggtgacttttaagcagtatctt---tctttttgcgactcatgactatctatatatcagGTTTCATTGTGCAACTACGAAGCCTAGAGGACCACTCTCCCCTTCCCGGTGTTACTCTTGGTGATATCGGCGGAAAATTTGGTAGTGGTGCATACAACAG

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 5
----------gtaagagtgttttgtgtttaggtgatatttaagtgttctcctagtctcctttgtttcttatgcacgtccttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG
          | || ||| |   || |||   |  | || || | ||||          ||  |||||||  |   |   | | ||||| ||||| |||||||||||||||||||| ||||| || ||||||||   ||| ||| | |||||||| ||   |||  | || | ||| ||||||||   
gtatgtaccgggaaaagtttccagtattttttttttgttcaatttttcttgcttgggtattgctttcttaaac---tttctcttccagGATTCATCGTGCAACTGCGAAGCTTAGAAGATCATTCTCCTCTTCCGAATATAACTGTTGGTGATATCGGGACAAAGATGGGAAATGGAGCATATAATTC
















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|78109870|gb|DV528286.1|DV528286
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|78092061|gb|DV520435.1|DV520435
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|78118216|gb|DV536603.1|DV536603
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGTCA-CTGCGAAGCTTAGAGGATCACTCTCCTCTTCCTGGT
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTG-CAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGT
EST: gi|149044450|gb|EE047571.2|EE047571
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|148952746|gb|EC898728.2|EC898728
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGATA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|149089538|gb|EE178785.2|EE178785
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|32934681|gb|CF039493.1|CF039493
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAACTTAGAGGATCACTCCCCTCTTCCTGGTA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|213184355|gb|FM193741.1|FM193741
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|149096635|gb|EE182400.2|EE182400
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|78089952|gb|DV518326.1|DV518326
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|211132734|gb|FL016682.1|FL016682
EST:     GATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTG
genomic: GATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|211132737|gb|FL016685.1|FL016685
EST:     GATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGCAACTGCGAAGCTTANAGGATCACTCCCCTCTTCCTGGTG
genomic: GATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTA
EST: gi|149106570|gb|EE188463.2|EE188463
EST:     AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG                         GTTTCATTGTGNCA-CTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGT
genomic: AGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTG-CAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGT

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: 46 (upstream exon), 49 (downstream exon)
Score: 275

TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 915

TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 667

TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1268

TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATGgtaagagtgt ... cttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatttaagtgttctcctagtctcctttgtttcttatgcacgtccttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG
                                           tccttgtccc  CT-rich tract
                              tttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagtgttttgtgtttaggtgatatttaagtgttctcctagtctcctttgtttcttatgcacgtccttgtcccagGTTTCATTGTGCAACTGCGAAGCTTAGAGGATCACTCCCCTCTTCCTGGTATTACTCTGGGTGATATTGGTGGAAAATTTGGCAGTGGTGCATATAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA