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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

Basic information

species Zea mays
transcript GRMZM2G416836_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
||||   || | | | || ||  ||| ||   |||| | |||| |||  |||||| |||| ||||||||||||||| |||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| ||||| ||||||||||| |||||||||||||||||||
gtaaatgctcaatatcttttttggataaatacttcaaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA

upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
---------gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
            |  |  |||  |   ||||  ||  |      |  |||   | | | |||    |  ||  |  || |||||  |||||||||||||||| |||||||| || || || ||| |||| || |||||||||||||||||||||||||| || || ||||| |||||||| |
gtacatgtccagagatacaaccatgacattcc-atacagccgcaatgtttactgtatacttag--gtttattttctat-cagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
--------------gta-atgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
               || | ||  |||  ||  |||| | |    |  |  | ||||       ||  ||  |  ||  |  || |||||  |||||||||||||||| ||||| || || || || ||| | || || |||||||||||||| ||||||||||| || || ||||| |||||||| |
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttactt--atggtttattttctat-cagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
--------------------------------------------gtaatgtctaactgttttattctgatgaaattttcagatttcaa---gaagatttaatcatgcatcc--ttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                                              |||    |    |      || |||||| | |  || |   |   |||| |  |  |||   |||  ||| |||||||  ||||||| |||||||| || |||||||| ||||| || || |||||||| |||||||||||||| || || ||||| || ||||| || || |  |
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA

upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 20
-----------------------------------------------gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatcctt---catgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                                                 ||  | |        || |||  | || | ||  | ||     ||  |  |   |   |   ||   | |  ||||| ||||||||||||||||||| |||||||||||||| ||||| || || || ||||| || |||||| |||| || || ||||||||||| || || |
gtatatattatctatatgaacttaaaaaaagccacaagatttctaactgaaaatgttctcacactaatctagtaaactcttttggttgttctaatttccacaaaaaaactattggccttatagGTGATGACAACATTCATGCCGCCTCCACCAGCATCAACGTTTTTGGCGTTCCATCCTCAGGACAATAACGTCATCGCCATTGGAATGGAAGACTCTACGA

upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
-------gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagattta--atcatgcatccttcat--gcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
         ||  ||  | | ||  ||  | || ||||||   |  ||  | | | ||||  || |||   | |||||  | ||||  |||||||||||||| | || || || || ||||| ||  |||| || || |||||||| |||||||||||||| ||||||||||| ||||| ||||
gtatgtctaaacatcacagttttgcatcttcatcaaattt--ggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA

upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
------------------------gtaatgtctaactgtt-ttattctgatgaaattttcagatttcaag---aagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                         || | |  ||   ||  | | ||| |||   ||  | ||  ||      | | ||      | ||  |  || |||||  |||| ||||||||||||||||| |||||| | || ||| | || || || || ||||| || |||||||| || ||||||||||| |||||||| |
tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtg-attcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
---------------------------------------------------------gtaatgtctaactgtt--ttattctgatgaaattttcagatttcaagaagat-ttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                                                         | |  || |   | ||  | ||| |||   | || |||  ||| |    ||   |  || |      || |  |||||  |||| ||||||||||| ||||| |||||| | || ||| | |||||||| || ||||| || || ||||| || || |||||||||||||| || |
gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgac--agttgtcaatttttattctgacgcttttcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

upper sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                        ||| |  |||    ||       | | |||     | | |    | |||||| ||||| |||||||||| || ||||||||| |||| ||  | || |||||||||||||| || || |||||||| || |||||||||||||| || |
----------------------gtatgcacatttttccttcttgaccggtgtaa--gaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

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: 39 (upstream exon), 43 (downstream exon)
Score: 17

AGAGGAGGCAATCCCATGCATTGCACTCTCCAAGAATGATTCCTATGTGATGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTACCATGATGACATTTAAGgtaatgtcta ... cttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 84

AGAGGAGGCAATCCCATGCATTGCACTCTCCAAGAATGATTCCTATGTGATGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTACCATGATGACATTTAAGgtaatgtcta ... cttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 69

AGAGGAGGCAATCCCATGCATTGCACTCTCCAAGAATGATTCCTATGTGATGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTACCATGATGACATTTAAGgtaatgtcta ... cttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

AGAGGAGGCAATCCCATGCATTGCACTCTCCAAGAATGATTCCTATGTGATGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTACCATGATGACATTTAAGgtaatgtcta ... cttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                                         catccttc  CT-rich tract
         aaattttcagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA