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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgtagcacaaagttattgttctcttgagtctagaatataaacttttcaatcagctgttactgttggtggattactcaaagattttatgtttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC

Basic information

species Zea mays
transcript GRMZM2G077187_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g49820.2 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------------------------ttcgtagcacaaagt---tattgttctcttgagtctagaatataaacttttcaatcagctgttactgttggtggattact---------caaagattttatgtttatctt---agGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC
                                                                             || | |  |  ||     ||   ||      | |||||| |  ||    ||  |   ||||       | ||||| ||||           | || ||||| ||| | |    ||||||||||||||||||||| ||||| ||||||||| ||||||||||||| ||||| || ||  | ||||| |||||||||||| |||||||| |  ||  
gtaagtgaattctgtcagttgataatttcgtatgtatttctctaccttgttactacgaaatctcagtggaatttcagttagcattatcaaacacataggattggtcatactctagactgcaagagcttttacgtgctgcctgctcttgtggagtactgtggatcgctgacgaatttatttttgtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAAAAGTTTTTGACAGAAGAGGCCATGTTGCAAAACTCTGCATTATTATTCT

upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G29390.1 (Glycine max), 3'ss of exon 6
----ttcgtagcacaaagttattgttctcttgagtctagaatat-aaacttttcaatcagctgttactgttggtggattactcaaagattttatgtttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC
    | |  | | ||   ||   | |    | |   | |||||| ||| || |||||  |  ||   ||||  |   | | |     |||      | |    |||||| |||||||||||||| |||||||||||||| ||  |  | ||| | | ||| || |||||||| ||  || |||  ||| | ||| | ||| |   
acggtcctaatcccagtcttgaaggttgtctaaccattgaatatgaaaattatcaatt-gtggtatgtgtttttttttaatttggtaatt----aataaatgcagGGTCCTTTGCTGGCCTTGGTTTCCTTTCATGGTACTTATCAAGGAAAGTTAGAGTGTTTGATCGTAGGGGCAATATTGGGAAACTATGCCTAGTCTTGCT
















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|113703064|gb|EE680568.1|EE680568
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|78124930|gb|DV543314.1|DV543314
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|24934593|gb|CA452811.1|CA452811
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|14243380|gb|BG841070.2|BG841070
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|86467942|gb|DY234312.1|DY234312
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|113701660|gb|EE679164.1|EE679164
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|61119018|gb|DN559979.1|DN559979
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGCTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|78079032|gb|DV507444.1|DV507444
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|76282157|gb|DV021725.1|DV021725
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCA
EST: gi|76289091|gb|DV028659.1|DV028659
EST:     GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCAT                         GGTCTTTTGCTGGCCTTGG
genomic: GAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGG

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: 40 (upstream exon), 44 (downstream exon)
Score: 7

GAGTATAACAACTTTACTACAGGCGCCATATGCCATGGCCAGGCGAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 237

GAGTATAACAACTTTACTACAGGCGCCATATGCCATGGCCAGGCGAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

GAGTATAACAACTTTACTACAGGCGCCATATGCCATGGCCAGGCGAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 8

GAGTATAACAACTTTACTACAGGCGCCATATGCCATGGCCAGGCGAGTGTTATTAAAGAAGGTCATAAAAGCTTTCCAAGTGGTCATACTTCATgtaagtgaca ... tttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaatcagctgttactgttggtggattactcaaagattttatgtttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC
                                             tttatctt  CT-rich tract
                                 aaagattttatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgtagcacaaagttattgttctcttgagtctagaatataaacttttcaatcagctgttactgttggtggattactcaaagattttatgtttatcttagGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- -gtagcac
- - - - - - - - - - - - - - - - - - - - - - - - - -tcagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actcaaa