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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatatttctaaattttggccacagtcagtagtcatactgtgtcttgggtacccatagccctaaatgtactgaaatgattttgcaactccttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT

Basic information

species Zea mays
transcript GRMZM2G174757_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 9
gtatatttctaaa--ttttggccacagtcagtagtcatactgtgtcttgggtacccata-gccctaaatgtactgaaatgattttgcaactccttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT
 | | ||| |||   || |  |    || | ||  ||   |  |   ||| |  || |      ||   | ||| ||||||| |||  | |  ||||    |||||||| ||  |||||||||||||||| ||||||||||||||||| || ||||||||||| |||||||||||||| |||||||||||||||||||| || 
-tttttttataatacttctcactggtgtgactaaacaagttaaga--tggatttccttgtatgttagtggaactaaaatgatgttgggatttttttttgttagATATCTTGCATCTGCAGTTACCTCAGTCCATGAAATGGAGAATGGTTTCCAAATATGGTCTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCAC

upper sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------------------------gtatatttctaaat--tttggccacagtcagtagtcatactgtgtcttgggtacccatagcc------ctaaatgtactgaaatgattttgcaactccttt-tgtc-cagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT
                                                                                   |||| |  || | |  ||  |   | |    | | ||   |         || |  || |         ||| | | |  |  | || ||||     |||| | |  ||||||| | || |||||||| || ||||||||||||||||||||||| ||  | |||||||| |||| |||||||||||| ||   | |    |||||||||
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagttcataggttaatcttttgtaaaatcagtttaaaattgtatttaccttagtcattaagtgtctgatttttgccactttactgaaaaagtgcttattgttggtttgttaattatcccaagcttatattgctttctctttatatggcagATATGTTGCAACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAT

upper sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------------------------------------------gtatatttctaaattttggccacagtcagtagtcatactgtgtcttgggtacccatagc------cctaaatgtactgaaatgattttgcaactccttttgtcc--agATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT
                                                                                      | ||  | |    |   |     |  | | |  ||  |         || |  || |       | ||| | | |  |  | || ||||     ||||   |   |||||| | || ||||| || || ||||||||||||||||||||||| ||  | |||||||| |||| |||||||||||| ||   | |    |||||||| 
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaagcttatattgctttctctttatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC

upper sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------------------------gtatatttctaaattttgg-----ccacagtcagtagtcatactgtgtcttgggtacccatagccctaaatgtact---gaaatgattttgcaactccttttgtcc--agATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT
                                                              ||| | |||     ||       | |    | ||| ||| |  |  | || |  |    |     |   ||||     |   |||| ||  ||||| ||   ||   || ||| | || ||| ||||||| ||||||||||| ||||| ||||||||| | |||||||||||||  |||||||  || ||   | |   ||||||||| 
gtagttttggaagaactattatattgttttgttttctaaatgaaatatcagttatcttacaatatttatcttgtccttaaaaattcgatttcctgtaatcagaaggaat-ttagtcatttgttctattgcttgtatcttggctgtgatatt-taactctttgcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCAC

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|76289751|gb|DV029319.1|DV029319
EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTT
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTT
EST: gi|32929764|gb|CF034576.1|CF034576
EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTGCCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
EST: gi|6994119|gb|AW453333.1|AW453333
EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
EST: gi|6564113|gb|AW231735.1|AW231735
EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
EST: gi|32929752|gb|CF034564.1|CF034564
EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
EST: gi|149098248|gb|EE184214.2|EE184214
EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
EST: gi|21843249|gb|BQ703830.1|BQ703830
EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
EST: gi|32928528|gb|CF033340.1|CF033340
EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 311

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtacccatagccctaaatgtactgaaatgattttgcaactccttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT
             ccctaaa  putative branch site (score: 195)
                                         ctccttttgtcc  putative PPT
                           aaatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttctaaattttggccacagtcagtagtcatactgtgtcttgggtacccatagccctaaatgtactgaaatgattttgcaactccttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT

- - - - - - - - - - - - - - - - -catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca