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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttctacatttgcttttctgtgtacatcaatgcaatatggttgagaaaatgaaagcacaagataaacaaaataaaagctagtgggctttgatcaaa...

Basic information

species Zea mays
transcript GRMZM2G180815_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g44394.1 (Oryza sativa), 5'ss of exon 6
GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttctacatttgcttttctgtgtacatcaatgcaatatggttgagaaaatgaaagcacaagataaac---aaaataaaagctagtgg-gctttgatcaaa
||||||||||||||||||  ||||||||| || ||||||||||||||||||||||||||||||||||| ||||| ||| |||||||  ||   ||| || ||  || || ||   ||   |  | | ||            | ||  | | |    |  || |  ||| | |   | | |  |  
GCTGAATTCAAGAGGATTGTGTCACCTTTAAAACTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAGCAAGGGTTTCTGgtaatgcct-tgttttctctttggtctaaat--gtgggttccgttcgatgtttcttcctaataattttagctcccatgtacatcctaattgcaatctcagtag-

upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 6
GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaa------tttctacatttgcttt-tctgtgtacatcaatgcaatatggttgagaaaatgaaagcacaagataaacaaaataaaagctagtgggctttgatcaaa
| |||||||||||| |||   ||||| || |||   || |||||||| ||||||||||| ||||||||||||||||| ||||||       || |||  |||  ||| || ||| | |  |||   || |  ||   | | ||    |  |   |  |   |  ||   ||  |   || | |     
GTTGAATTCAAGAGAATTGTTTCACCATTAAAGTATCAAACAAGGTGCCTTGCTGCATTCCCTGATCAACAAGGTTTCTTGgtatgcatctttcctatctttattttatcagtgaaaagtaatatcatgt--ttccaacagtgggttcctattttgtatctag-aaggacttattttctgtaac----

upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 6
GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgta-atttctacatttgcttttctgtgtacatcaatgcaat---atggttgagaaaatgaaagcacaagataaacaaaataaaagctagtgggctttgatcaaa
| |||||||||||| |||   ||||| ||||||   || |||||||| ||||||||||| ||||| ||||||||||| ||||||    |||       ||  | |  |  | ||||| |  |    |  ||| | || |  |    | |  |  |    || |    |     ||  |  |||| 
GTTGAATTCAAGAGAATTGTTTCACCCTTGAAGTATCAAACAAGGTGCCTTGCTGCATTCCCTGACCAACAAGGTTTCTTGgtatgcatctctccccactcctttaagatcttcaatcctgttccgtatttgggtaattttatttcccatctttattttatcag---tgaaaagcaatactcaa-

upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA01G09290.1 (Glycine max), 5'ss of exon 6
GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttctacatttgcttttctgtgtacatcaatgcaat-atggttgagaaaatgaaagcacaagataaacaaaataaaagctagtgggctttgatcaaa-----
 |||||| |||||| |||   || ||  ||||    ||||| || | | ||||||| ||||| |||||||||||||||||||||     |  |||    | ||  | ||||| ||| |  |  | |  |    |||    ||      ||    |  |||   |      ||| ||||         
ACTGAATACAAGAGAATTGTATCTCCCCTGAAATATCAGACCAGATCTGTTGCTGCTTTTCCAGATCAACAAGGTTTTTTGgta-----tgtattcagctctcaat-tacattaatactcttgtagaagtcctaattgttgccttctttattttatttaatctcattacagctatgatatggggcaa

upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA02G13780.1 (Glycine max), 5'ss of exon 6
GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgta---attt---------ctacatttgcttttctgtgtacatc---aatgcaatatggttgagaaaatgaaagcacaagataaacaaaataaaag------ctagtgggctttgatcaaa--------------------------------------------------------------------------
 |||||| |||||| ||    || ||  ||||    ||||| || | | ||||||| ||||| |||||||||||||||||||||   |||           || |||        |||  |  ||   | ||     |  || |    ||  || | ||  |     |  |||   |      ||  |     |||||||||                                                                          
ACTGAATACAAGAGAATCGTATCTCCCCTGAAATATCAGACCAGATCTGTTGCTGCTTTTCCAGATCAACAAGGTTTTTTGgtatgtattcagctctcaattatattaataaacttgtagaagtcttaattgttgccttctttattttatttaatctcattactgctatgatatggggcaattcttatcactattgatcaaatctcttgctgtatattcacttaaaaatttgaatttctggcattatggagtattgactatactgtttctctgtag

upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 7
GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaa---tttctacatttgcttttctgtgtac--atcaatgcaatatggttgagaa-aatgaaagcacaagataaacaaaataaaagctagtgggctttgatcaaa
 |||| || ||||| ||    || ||  |||||  |||||| |||||| || |||| || |||||||| |||||||||||||||    ||  ||  | || | |  |||||     | ||| || | |    |  |  |       |   ||||    | | |  | | |||    | |||  ||| 
ACTGAGTTTAAGAGAATCCAATCCCCACTGAAGTACCAGACGAGGTGTGTTACTGCCTTCCCTGATCAGCAAGGTTTTTTGgtatgtcttcttatttatgttctgttgtgttttggttaattcagttttacaggaattagcttgttcgttagatgcttacattttaggttag---acattg--caa-

upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 5'ss of exon 6
GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaa-tttctacattt-----gcttttctgtgtacatcaatgcaatatggttgagaaaatgaaagcacaagataaacaaaataaaagctagtgggctttgatcaaa
 | || || ||||| || || |||||  |||||   |||||||| ||| |||| |||||||||||||| |||||||| || |||| | | |   |||     | |||| ||| |   | | | | |  |  ||      | |||  |   |  |   |    |  |   |  | || |||       
ACCGAGTTTAAGAGAATCACTTCACCCCTGAAGTATCAGACAAGATGTGTTGCAGCATTTCCTGATCAGCAAGGTTTCTTAgtaagtctttgtttttatttagtttttttgtctctctaatttctacttcatttttctgaagaattcttgatttcttctttcttcatcttgtttggttttc------

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|50331331|gb|CO526457.1|CO526457
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|84969286|gb|DW467729.1|DW467729
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|91875720|gb|EB405677.1|EB405677
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|88757959|gb|DY542100.1|DY542100
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|71448754|gb|DR829804.1|DR829804
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|78073884|gb|DV502318.1|DV502318
EST:     TCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: TCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|78073885|gb|DV502319.1|DV502319
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|88758075|gb|DY542216.1|DY542216
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|71758084|gb|DR956021.1|DR956021
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|74234227|gb|DT642141.1|DT642141
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|71432893|gb|DR813943.1|DR813943
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|71432894|gb|DR813944.1|DR813944
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAAGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|50332450|gb|CO527576.1|CO527576
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|71763057|gb|DR960994.1|DR960994
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|29543837|gb|CB604217.1|CB604217
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|74240564|gb|DT648478.1|DT648478
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|76930213|gb|DV172299.1|DV172299
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
EST: gi|76286199|gb|DV025767.1|DV025767
EST:     AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG                         ATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG
genomic: AGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAG

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: 127

GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAGCAAGGAAAAAACTTTACATTCAAGTGTCACCGCGATGGCAATGATATAT


Block sizes: 38 (upstream exon), 41 (downstream exon)
Score: 8

GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAGCAAGGAAAAAACTTTACATTCAAGTGTCACCGCGATGGCAATGATATAT


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 12

GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAGCAAGGAAAAAACTTTACATTCAAGTGTCACCGCGATGGCAATGATATAT


Block sizes: 45 (upstream exon), 38 (downstream exon)
Score: 22

GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttcta ... tgatttgaagATTGGGTCTATAGAAGGACGAGTTGGTGTTCATCATGTGGAAGAGTCTCAGCAAGGAAAAAACTTTACATTCAAGTGTCACCGCGATGGCAATGATATAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTGgtaatttctacatttgcttttctgtgtacatcaatgcaatatggttgagaaaatgaaagcacaagataaacaaaataaaagctagtgggctttgatcaaa

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataaa