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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCAAAGCTGGTGCACAATGTATACAGATCTTTGACTCTTGGGGTGGGCAGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattcattggcatcttgtattcatattttattccttttttcgtttatcttcttagagttcaaagaacagataacgcatattttaccaattcaaggctcggataaagtgcatgtcgttgctaaaattttgagcattgttctcggccaccgctctgaccttctagtcttcttttccag

Basic information

species Physcomitrella patens
transcript PP1S3_96V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S3_96V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G025031_T01 (Zea mays), 5'ss of exon 1
AGTCAAAGCTGGTGCACAATGTATACAGATCTTTGACTCTTGGGGTGGGCAGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattcattggcat-cttgtattcatattttattccttttttcgtttatct---tcttagagttcaaagaacagataacgcatattttaccaattcaaggctcggataaagtgcatgtcgttgctaaaattttgagcattgttctcggccaccgctctgaccttctagtcttcttttccag
||| ||  | || || || ||||||||||| ||||| || |||||||| |||||||| |||||   |||||| |||||||| || || |||||  | ||||||    ||| ||    | ||||  ||||| | |||     ||  | || |  ||   | |  |   |     |    ||||| |  ||    || | |                                                                                      
AGTTAACTCGGGGGCCCAGTGTATACAGATATTTGATTCATGGGGTGGACAGCTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAACAGgtgactcttccttacttttcttgctttcatgtattaccaacttcatggtgttgctatgtatctgcactgtcttatggtataacactgatgactcccactg-------------------------------------------------------------------------------------

upper sequence: PP1S3_96V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G024738_T02 (Zea mays), 5'ss of exon 3
AGTCAAAGCTGGTGCACAATGTATACAGATCTTTGACTCTTGGGGTGGGCAGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattcattggcat-cttgtattcatattttattccttttttcgtttatcttcttagagttcaaagaacagataacgcatattttaccaattcaaggctcggataaagtgcatgtcgttgctaaaattttgagcattgttctcggccaccgctctgaccttctagtcttcttttccag
||| ||  | || || || ||||||||||| ||||| || |||||||| |||||||| |||||   |||||| |||||||| || || |||||  | ||||||    ||| ||    | ||||  ||||| | |||     ||  | || |  ||   ||    |  |    |  ||     |    | |  | ||| |                                                                                   
AGTTAACTCGGGGGCCCAGTGTATACAGATATTTGATTCATGGGGTGGACAGCTTCCACCTCATGTGTGGGAGCAGTGGTCAAAACCATATATCAAACAGgtgactcttccttacttttcttgctttcatgtattaccaacttcatggtgttgctatgtat--ctgcactgtcttatggtataacactgatgacttccactg--------------------------------------------------------------------------------
















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|162196437|gb|FC375429.1|FC375429
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162215135|gb|FC390760.1|FC390760
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162219753|gb|FC395957.1|FC395957
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162265473|gb|FC440799.1|FC440799
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162239163|gb|FC416263.1|FC416263
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|7067513|gb|AW497368.1|AW497368
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|37847318|gb|BJ605326.1|BJ605326
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|37841761|gb|BJ599769.1|BJ599769
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162193871|gb|FC368733.1|FC368733
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162196438|gb|FC375430.1|FC375430
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTG
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTG
EST: gi|162197017|gb|FC375229.1|FC375229
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|18335025|gb|BJ167043.1|BJ167043
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|100416688|gb|BY993038.1|BY993038
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162239162|gb|FC416262.1|FC416262
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162219754|gb|FC395958.1|FC395958
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162193872|gb|FC368734.1|FC368734
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTG
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTG
EST: gi|162269779|gb|FC444932.1|FC444932
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|37824254|gb|BJ582320.1|BJ582320
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|37839889|gb|BJ597897.1|BJ597897
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162206181|gb|FC382251.1|FC382251
EST:     CGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: CGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|7067026|gb|AW496881.1|AW496881
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162160000|gb|FC335662.1|FC335662
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
EST: gi|162197016|gb|FC375228.1|FC375228
EST:     AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAG                         CTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC
genomic: AGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTAC

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 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 34 (downstream exon)
Score: 10

AGTCAAAGCTGGTGCACAATGTATACAGATCTTTGACTCTTGGGGTGGGCAGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattc ... tcttttccagCTTGTGGCCAAGGTGAGAGACGCTTGCCCGGGGGTACCATTGGTGATGTACATAAACGGGAACGGCGGCTTGCTCGAGAGGATGGCTACAGTTGATGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCAAAGCTGGTGCACAATGTATACAGATCTTTGACTCTTGGGGTGGGCAGCTTCCTCCTCACCAGTGGGATCAGTGGTCGAAGCCCTATATTCAGCAGgtgtaaattcattggcatcttgtattcatattttattccttttttcgtttatcttcttagagttcaaagaacagataacgcatattttaccaattcaaggctcggataaagtgcatgtcgttgctaaaattttgagcattgttctcggccaccgctctgaccttctagtcttcttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC