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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag

Basic information

species Zea mays
transcript GRMZM2G395549_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatat-ttctttctgacatagctgctctttttttgtttag
                                                                        |||||||||||||||||| |||||||| |||||||||||||||||||| |  ||||||||||| || ||||||||||||||||||||||||||||| ||| |||| |   |||||     || ||  ||    |||     | ||| | | |||   || | | || ||  || ||||| |||        | |||||||| |||
------------------------------------------------------------------------GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacaggagca---acctg--ttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacac-------ccttttttgtatag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatat-ttctttctgacatagctgctctttttttgtttag
                                                                        |||||||||||||||||| |||||||| |||||||||||||||||||| |  ||||||||||| || ||||||||||||||||||||||||||||| ||| |||| |   ||||   |  || ||  ||    |||     | ||| | | |||   || | | || ||  || ||||| |||      |  ||||||||| |||
------------------------------------------------------------------------GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacagga---ccaacctg--ttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacac-----ccttttttttgtatag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 23
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacat-agctgctctttttttgtttag-
                                                                         ||||||||||| ||||| |||||||| || |||||||| ||||||||||  |||||||||||| | || || |||||||| || || |||||| ||||| || | | ||  |   |  | |    | ||   |||   ||||   |       | ||| | |    |  ||  ||| |  || | ||| | |    ||    || 
------------------------------------------------------------------------AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCAGAGGAGTTCCGTTTGGCCCAGATATGTGGGCTTAACATTATTATTCAGgta-atatgtttgtttgt-tgccaagtcttcaactaaattttgaaatgaactggaatttgttt----ttctttattcagctatcatctgatttacaattagaaagt

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatg-atatatttctttctgacatagctgctctttttttgtttag---
                                                                         ||||||||| | || || |||||||| || ||||||||||||||||| | ||||||||| ||| | || || || ||||| ||||| |||||||||||| || | | || |      ||    | |||||   |   || ||| |   ||   | | | |||  |||||      |||  | ||  | ||  |         ||   
------------------------------------------------------------------------AGCTAACAGTTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCGGAGGAGTTTCGTTTGGCCCAGATTTGTGGACTCAACATTATTGTTCAGgta-atatgttg------atttcagtttttttgatgaactgtgtgtgtgtgtgta-tatatatatatataggaacgtctttcttaatttctgatgccagaccgagttc

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgtttta--ttgcaaagtttctatgatatatttctttctgacatagctgctcttt---ttttgtttag------
                                                                         ||||||||||| ||||| |||||||| || |||||||| |||||||||| ||||||||| ||| | || || |||||||| || ||||||||| ||||| ||               ||  ||| ||||| |||| ||||||  | |  ||  |||    ||   || | ||| | | | |   |||||   | |   ||    ||||      
------------------------------------------------------------------------AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-------------atatg-ttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttcttt-attcagctgtcatctgatttccagttagaaagtt

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag-----
                                                                         || |||||  | || || |||||||| || ||||||||||||||||| |  |||||||| ||| | || ||||| ||||| || || |||||| ||||| || | | || |          |   |||||   |   || ||| |        |    |     | ||| | |     || |   |  || ||| |  |  ||     
------------------------------------------------------------------------AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgta-atatgttgat-------ttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatatagg-aacgtttttcttcatttctgatgcagaccga

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatactt-----gatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag
                                                                         || |||||||| || || |||||||| |||||||||||||||||||| |  ||||| ||||| || || ||||| ||||| || || |||||  | ||| |  | || ||  ||  | || ||     ||   ||   || |  |  ||   || |||  |   | |  |||   | ||| | | ||   ||  ||||  | |     
------------------------------------------------------------------------AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCTGAGGAATTCCGACTGGCTCAAATCTGTGGACTTAACATTATCATACAGgtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatag-----

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtagg---agggcatacttgatttttccct----attctttgtttt--attgcaaagtttctatg-----atatatttc-tttctgacatagctgctctttttttgtttag---
                                                                         || |||||||| || || |||||||| |||||||||||||| ||||| |  ||||| |||||  | || |||||||||||||| || |||||  ||||| |  | |  |      |  |   ||   | ||| ||||      | || | |||  ||||   |   | |||      || ||| || ||| |  | | | |  ||||||  || |||    
------------------------------------------------------------------------AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGCGTTGATGCTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagata-------------tacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatg-atatatttctt--tctgacatagctgctctttttttgtttag-----------------------------------
                                                                        |||||||||  | || || ||||||||||| ||||||||||||||||| |  || ||||||||  | || || |||||||||||||| |||||| | ||| ||             ||   |||||  || ||  |    |  |    ||   ||||| | |   ||  |   | || ||    |||     || |  |    ||| |||| || |   |                                   
------------------------------------------------------------------------GGCTAACAGCTCAAAGACATGGAAGGAGGTTTGCTTTGCTTGTGTTGATGCAGAAGAGTTCCGCTTAGCTCAGATATGTGGTCTCAACATTATTATACAGgtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 12
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag-
                                                                        ||| || || ||    || |||||||| ||||||||||||||||| ||||  || |||||||| || || ||||| |||||||||||| ||||||| ||| |||  |         || |  |  ||||| |  |   | |  |  | || | | |   | ||| |   ||  || ||  ||||  || |||  |  |  | |  
------------------------------------------------------------------------GGCCAATAGCGCACGGACATGGAAGGAAGTCTGCTTTGCTTGTGTGGACGCCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatggataggtttctgc-tgttacattttgcaattagcctcatgattttactacgcaaccatgctt--ttcattactatcata--tgttctaatcgtactgaag

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 5'ss of exon 12
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattc--tttgttttattgcaaagtttctatgatatatttctttc--tgacatagctgctctttttttgtttag
                                                                        ||| ||||||||    ||||||||||| ||||||||||||||||| || |  || ||||| ||||| || ||||| |||||||||||| ||||||| ||| |||       | |  || |   | ||  |||   || |  |  ||||| |||     | | | |   |   |||||||  |||      || | |||  |  | |  
------------------------------------------------------------------------GGCCAACAGTGCACGGACGTGGAAGGAAGTCTGCTTTGCTTGTGTGGATGCCGAAGAGTTTCGTCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtat-------gaaaagcct-tctaatgcttcgacatccgatcagttttcttgagttttctgtttatcaaggttctttccttgattagtttgttgtttcatgatgtgc

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ13237 (Selaginella moellendorffii), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag
                                                                        ||| |||||||| || |||||||| || || ||||| ||||||||||||| ||| |||||| | || ||||||||||||||||||||  | ||||| ||| ||       |||      |   || || | | |||| ||||| ||  |  | ||  |  ||| | ||                                    
------------------------------------------------------------------------GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACGTCATTGTCCAGgta-------aggctatagtttctggttatactctat-ctttggttggt--ctaatctgttattaaatccag--------------------------------

upper sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag
                                                                        ||| |||||||| || |||||||| || || ||||| ||||||||||||| ||| |||||| | || |||||||||||||||||||| || ||||| ||| ||       |||      |   || || | | |||| ||||| ||  |  | ||  |  ||| | ||                                    
------------------------------------------------------------------------GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgta-------aggctatagtttctggttatactctat-ctttggttggt--ctaatctgttattaaatccag--------------------------------

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 2 RNA-Seq libraries.


Block sizes: 28 (upstream exon), 22 (downstream exon)
Score: 1

AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttg ... ttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC


Block sizes: 39 (upstream exon), 21 (downstream exon)
Score: 2

AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttg ... ttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACTGGGCTAAGCTGGCTGTTACCCTGGTTAAGCTGAAGCAATACCAAGGTGCTGTGGATGCTGCTCGCAAGGCTAACAGTGCTAAAACGTGGAAGGAGgtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG