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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca...

Basic information

species Physcomitrella patens
transcript PP1S438_29V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 10
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagt------------gtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca--------------------------------------------------
  | |  || || ||  |  || || |||| ||  |  | || ||||| ||||||||||||||||||||||||||||| || || |||||| | ||||||||      |   |    |       |     | |    |||                 ||  ||    |||    ||||   ||   || ||||   ||     | |                                                       
TCTTACACCCTCTGTTATCTCATTGATGGGTGGACTACTCCCCTTCGGCAGCATCTTCATCGAGATGTACTTTGTGTTTACTTCATTCTGGAACTACAAGgtaaagaaaacatatcagtgaacactaatgtgcttctcagttctcacttctcaacaaattattttgctagaacagatggcatttacagtagatgtgtaccaacctaaaactctttttaatttgatggatagatagtaaccctatttctttggtatttggcag

upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 5'ss of exon 10
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtgga--ggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca--
| | |  ||||| ||  |  || || |||| ||| || | || || || || |||||||| ||||||||||||||||||||||| |||||| | ||||||||     |      |  ||    |  ||    |  | ||||      || |  ||   |  ||| |  ||  ||     |  |  |    || || |       
CCTTACACCTTCTGTTATCTCATTGATGGGTGGGCTGCTTCCCTTTGGCAGTATCTTCATTGAGATGTACTTTGTGTTCACGTCATTCTGGAACTACAAGgtaaacagtttaacttaagtatccaagt--ttgttttggaaacagaagtag--tgcctatggtgtactggtgttcaacctcttatatggctgcttcataaatta

upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 10
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca-
| | | |||||| ||  | || ||  |||||||  || | || || || ||||||||||| |||||||||||||| ||||| || || ||| | ||||||||      |||    |   |         |  | |   | |     |  |  |  | ||| |    |   | ||  |   |   ||    | |   | || 
CCTCACGCCTTCTGTCATTGCCCTCATGGGAGGACTGCTTCCTTTTGGTAGCATCTTCATTGAGATGTACTTTGTCTTCACATCATTTTGGAACTACAAGgtaaa-acaggcaacactaattttcccatacaggcttcattac---taaggagccctgagagttgagacttatgcatccttcctgat-catctattgacag

upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 10
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctt-tgggttg-atggag-acgtgtttgagggca---
| | |  ||||| ||  |  || || |||| ||  || | || ||||| ||||||||||| |||||||||||||||||||| || |||||| | || |||||            |     ||   |     | |  ||  |   ||     |   ||  |  ||  | |||  ||   || | |  |  | ||||||         
CCTTACACCTTCTGTCATCTCATTGATGGGTGGCCTGCTTCCCTTCGGTAGCATCTTCATTGAGATGTACTTTGTGTTCACATCATTCTGGAACTATAAGgtaaacaa------gcaaatgcttttttacagttttgacctccttgagaccttgacattgctcactgtgctcctgtactgtacgttgtgcatgtttggtttttttt

upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 10
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggagg---ttggagggagcgg-gtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca-----------------------------------------
| | |  ||||| ||  |  ||||| |||| ||  |  | || ||||| ||||||||||| ||||||||||| || ||||| || |||||| | ||||||||      |     | |  | ||  |  ||   |  |    ||      |    | ||      ||||      | | |||    | ||    ||||                                                
CCTTACACCTTCTGTTATTTCACTGATGGGTGGACTTCTCCCCTTCGGCAGCATCTTCATTGAGATGTACTTCGTATTCACTTCCTTCTGGAACTACAAGgtaaaaaaaaaacatagtggtgattgaagtactaaagatccaatcaccagcatatagaatgatctgcactactttcttggtcacagtagcaaagtttctttcttttagtttcaaggaatattgactccacttggtgccttggcag

upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca------
| | |  || || || ||  | ||| |||||||  || | || || || ||||| |||||||||||||| ||||| ||||| || |||||| | ||||||||| ||  |  |    |  |     |  | ||| |  ||  |  | ||  ||   |    ||  |||  |    |||| |     || | |||   | |       
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaaat----gcaattacttttctgggccataaaagattattttttcttccctttgtttggtaca--aggtttacttttacttttttagagccgagccaa

upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca------
| | |  || || || ||  | ||| |||||||  || | || || || ||||| |||||||||||||| ||||| ||||| || |||||| | |||||||||  |  |  |    |  |     |  | |||  | ||  || | ||  |         ||  |  ||  |   ||| |     || | |||| | |||      
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaat----gcaattacttttctgggcagtaaaagtttattattctcttcccttg-gtttggtataaagtttacttctacttttttg-gagcagagcca

upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 10
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggtt------ggagggagcgggtggcagggtcggaagtgtgtgtt--ggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca
|||||  || || || ||  | ||| |||| || ||| | || || || ||||||||||| |||||||||||||| ||||| || |||||| | ||||||||   |  || ||        | | |    ||    |  | | || |   | ||    |||  || |  | |  | | ||||  | |   |||||   | | |     
CTTGACTCCATCAGTCGTCTCCCTGATGGGGGGTTTGCTACCCTTTGGAAGCATCTTCATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAGgtaaatatagtttctcttaataagaacaaagttatggaattgcaaattcttattccaattggccaaaccgga--gagatttgattagtgagagac---tctcaac---

upper sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 11
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca
  | ||||| ||  | ||||| ||  ||||||| ||  | || ||||||||||||||||| |||||||| || ||||||||||| || ||| | ||||||||                 | | |||  |  |  | |   | |  ||  | ||| | |||| | ||| || | |                          
TCTCAAGCCATCCATCGTGGCGCTTATGGGAGGCTTACTCCCATTCGGGAGCATCTTCATAGAGATGTATTTCGTGTTCACGTCCTTTTGGAACTACAAGgta----------------acccggt--cgagcccagttttttcagtctgctgatctgagtccgtggtgcatggcag-----------------------

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|37839289|gb|BJ597297.1|BJ597297
EST:     GGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|162198386|gb|FC372647.1|FC372647
EST:     GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|18339069|gb|BJ171095.1|BJ171095
EST:     TTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: TTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|37835139|gb|BJ593151.1|BJ593151
EST:     TCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: TCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|37829656|gb|BJ587668.1|BJ587668
EST:     GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|67725470|gb|BJ975729.1|BJ975729
EST:     GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|37840480|gb|BJ598488.1|BJ598488
EST:     GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|37848763|gb|BJ606771.1|BJ606771
EST:     CACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: CACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|37828715|gb|BJ586727.1|BJ586727
EST:     GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|37823937|gb|BJ582003.1|BJ582003
EST:     TGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: TGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|37831542|gb|BJ589554.1|BJ589554
EST:     GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|208364021|gb|DC950369.1|DC950369
EST:     TTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGNCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: TTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|162179316|gb|FC356265.1|FC356265
EST:     GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|18337178|gb|BJ169202.1|BJ169202
EST:     CTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: CTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
EST: gi|208373763|gb|DC936562.1|DC936562
EST:     GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAG                         GTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC
genomic: GCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATC

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: 35 (upstream exon), 32 (downstream exon)
Score: 21

CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggag ... gtttgtgtagGTGTACTACGTGTACGGATTCATGCTGCTGGTGTTCATCATCTTGACGATCGTGACGGTGTGCGTGACGATCGTGGGGACGTATTTCTTGCTGAATGCGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG