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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttcccggtaggctgtttatgtagtacatattgatttttttttcgatttcacttgcag

Basic information

species Zea mays
transcript GRMZM2G391936_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 5'ss of exon 5
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaa-------------ataaattttcccggtaggctgtttatgtagtacatattgatttttttttcg-atttcacttgcag
||||| ||| |||||||||| || ||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||              || | || |    || ||||||| | |||||| || |  |||  ||||  | ||   | || |||
GATGCCAAAGCTAAAGACATCGATGATGTGCTGATTCTTTCTGGTGATCATCTCTACCGCATGGACTACATGGACTTTGTTCAGgtaattgtctgtacatacatcatttcttgtagttggctgttaaagtagtatatttgaattgattttgggtatccaatttacag

upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G38820.1 (Glycine max), 5'ss of exon 5
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttc--ccggtaggctgtttatgtagtacatattgatttttttttcg-atttcacttgcag----------------------------------
||| ||| |  ||| || ||||| |||||  |||||||||| || || || |||||||| |||||||| |||||||||||||| ||||   |   |  |  ||  |       || |      | | |  |||   ||   | |||  | |||  |                                  
GATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAAgtaaggcactgtgccatccaatcaaacaattctcc--cccctttcaattcagttgatgcattcaaattgttgactctcagatgttttgactccttttcatatccag

upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA17G01900.1 (Glycine max), 5'ss of exon 5
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttc--ccggtaggctgtttatgtagtacatattgatttttttttcgatttcacttgcag----------------------------------
||| ||| |  ||| || ||||| |||||  ||||||||||||| || || |||||||| |||||||| |||||||||||||| ||||   |   |  |  ||  |    |  || | |    | |   | ||  ||  |  |||  | |||  |                                  
GATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAAgtaaggcactgtgccatccaatcaaataattctctccccctttcagtttagttgatacattcaaattgttgactctcagatgttttgactcattttcatatccag

upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 5'ss of exon 5
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttcccggtaggctgtttatgtagtacatattgatttttttttcgatttcacttgcag------------------------
|||  || |  ||| || ||||| |||||||||||||| ||||| || ||| | ||||| |||||||| ||||||||||||||||||| | |        |  |  |   ||| |||  |  || |   ||  ||||   | | |||| | |                         
GATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAGgtaagacactgccattcactttg--atttctgttcttgat-tcatttcattttattagtacactcggaaacattttatctgctttatttccag

upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: PP1S389_5V6.1 (Physcomitrella patens), 5'ss of exon 4
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttcccggt---aggctgtttatgtagtacatattgattt---ttttttcgatt--tcacttgcag-----------------------------------------------------------------------------------------------------
||||| ||   ||| |   | ||||| ||  | ||| | || || |||||| | |||||||||||||||||||||||||||||||||||       | ||  ||   |   ||||    | | ||  || | |     |   |  | ||  ||||    ||                                                                                                     
GATGCCAAGAATAAGGTTGTGGAAGACGTAGTAATTTTATCCGGAGACCATTTGTACCGTATGGACTACATGGACTTTGTTCAGgtaaatcctcagtcccgtgttcaattttgttgtcattgaactcatagctacaaataactctggttgttcaccgctagtcatctgaatttgtactcaagttttttcaaatgaagatctcaagaggcgtgtgatttggtagcaaggttcctcacagtgtcttgttttacgcatttgacag

upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: PP1S2_204V6.1 (Physcomitrella patens), 5'ss of exon 4
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaa-taaattttcccggtaggctgttt---atgtagtacatattg----atttttttttcgatttcacttgcag--------------------------------------------------------------------------------------------------------------------
||||| ||   |||||   | || || ||  | ||  | || || || ||||| || ||||||||||||||||||||||| ||||||||  |  |   |  || | | | || |   || |   |||| ||     || |  |  |||||||       ||                                                                                                                    
GATGCGAAGAATAAAGTTGTAGAGGACGTTGTAATCTTGTCCGGAGATCATCTTTATCGTATGGACTACATGGACTTTGTCCAGgtaaacctccaaccttacgtttgaccgtctcctattttcaacatttttcaatatgtgctgctcgattttcaacagagatgtcaatgctcaagtgattggttactaggtcctaggattccggaattatggccgaggccaagatgatggctaactacaggaattctgatattgttttgtttttttcatataatag

upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: PP1S347_12V6.1 (Physcomitrella patens), 5'ss of exon 5
-----------------GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTC----TACCGTATGGACTACATGGACTT----TGTTCAGgtaaaataaattttcccggtaggctgttt----atgtagtacatattgatttttttttcg-atttcacttgcag------------------
                   |    | |  |  ||| |||   |   ||  |       ||||| | || ||    || | |  |  |  |||||||      | |||||   ||  | |   ||| |     | || |    ||  | | |  || || ||  |||    | || |||| |||                  
CCGGCGATCACCTCTACCGTATGGATTACATGGACTTTGTCCAGAAGCACAGGGACAGTGGTGCCGATATCACAATATCTTGCGTGCC-CATGGACGACAGgtattcagtggaaccacaacatccagaatttccgtctgagaattcactgctgatggacttggtttctacagtttacttacagattagtgactgtagtatt

upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 6
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttcccggtaggctgttta---tgtagtacatattgatttttttttcg-----atttcacttgcag
||||  | |   || ||| | ||  | |||||  |||| || ||||| || |||||||| |||||||||||||||||||| ||||||   |   | || |  | ||  ||| |    |||     || |   |  | |  | |      || | |  ||||
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttt--tcttgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatggtggctggcgttgctcccgcag

upper sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
lower sequence: EFJ25399 (Selaginella moellendorffii), 5'ss of exon 5
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttcccggtaggctgttta---tgtagtacatattgatttttttttcg-----atttcacttgcag
||||  | |   || ||| | ||  | |||||  |||| || ||||| || |||||||| |||||||||||||||||||| ||||||   |   || | |  | ||  ||| |    |||     || |   |  | |  | |      || | |  ||||
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttatgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatggtggttggcgttgctcccgcag

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|211493116|gb|FL031298.1|FL031298
EST:     TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGAT
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGAT
EST: gi|32934983|gb|CF039795.1|CF039795
EST:     TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGAT
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGAT
EST: gi|149101455|gb|EE187574.2|EE187574
EST:     TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAGGTGCAGGCATCAGCATC
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATC
EST: gi|71429963|gb|DR811013.1|DR811013
EST:     TTCTTTCTGGGGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAA
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAA
EST: gi|71435811|gb|DR816861.1|DR816861
EST:     TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGA
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGA
EST: gi|211114649|gb|FL303211.1|FL303211
EST:     TTCTTTCTG-TGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAG-TGCAGGCATCAGCATC
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATC
EST: gi|211118620|gb|FL303281.1|FL303281
EST:     TTCTTTCTG-TGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAG-TGCAGGCATCAGCATC
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATC
EST: gi|32934981|gb|CF039793.1|CF039793
EST:     TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGAT
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGAT

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 3 RNA-Seq libraries.


Block sizes: 33 (upstream exon), 41 (downstream exon)
Score: 11

GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGATGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGATGGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGATGGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttcccggtaggctgtttatgtagtacatattgatttttttttcgatttcacttgcag

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