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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTGGGCTTTAAGCAAGTACTATCCTCATGTGAAGACGTTTGTGCGTGCTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctggctccgaagggttttggtctagttaaagtatcattatgtgttgcatatgattgcaagaattagaggtgtgaacagtggagcactataggt...

Basic information

species Physcomitrella patens
transcript PP1S2_217V6.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_217V6.1 (Physcomitrella patens), 5'ss of exon 20
lower sequence: GLYMA09G39770.1 (Glycine max), 5'ss of exon 21
GGTGTGGGCTTTAAGCAAGTACTATCCTCATGTGAAGACGTTTGTGCGTGCTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgta-tgttctggctccga----agggttttggtctagttaaagtatcattatgtgttgcatatgattgcaagaattagaggtgtgaacagtggagcactataggt
 || |||||||||||||||||||  ||  |||||||||| ||||| ||||| ||||| || ||||||||| ||| ||| || ||||||||||| ||||| ||| | ||||    || |    || |||      | | | |  |     ||    ||  | ||  | | |  | ||   |||    ||| |  ||||    |   
AGTTTGGGCTTTAAGCAAGTACTTCCCAAATGTGAAGACTTTTGTTCGTGCCCATGACGTTGATCATGGATTGAATTTAGAAAAGGCTGGAGCTACTGCTgtaatattctcatacctattctagcgttccccgtttgattacctgatggtacaatttcaaaatagtggtagcattt---ggtaaacacattcaagcatctgaa--

upper sequence: PP1S2_217V6.1 (Physcomitrella patens), 5'ss of exon 20
lower sequence: GLYMA18G46420.1 (Glycine max), 5'ss of exon 25
GGTGTGGGCTTTAAGCAAGTACTATCCTCATGTGAAGACGTTTGTGCGTGCTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgta-tgttctggctccga----agggttttggtctagttaaagtatcattatgtgttgcatatgattgcaagaattagaggtgtgaacagtggagcactataggt
 || |||||||| ||||||||||  ||  |||||||||| ||||| ||||| |||||||| ||||||||| | | ||| || ||||||||||| ||||| ||| | ||||    || |    || |||      | | |    |     ||    || || || | ||  || ||| |     ||  || |  | |     | | 
-GTTTGGGCTTTGAGCAAGTACTTCCCAAATGTGAAGACTTTTGTTCGTGCCCATGATGTTGATCATGGATTAAATTTAGAAAAGGCTGGAGCTACTGCTGtaatattctcatacctattttagtgttccccgtttgattggctgatggtaca-atttcaaattactggtagcatttggtaaatg--cattcaaacgtctgaag-

upper sequence: PP1S2_217V6.1 (Physcomitrella patens), 5'ss of exon 20
lower sequence: GLYMA07G08030.1 (Glycine max), 5'ss of exon 17
GGTGTGGGCTTTAAGCAAGTACTATCCTCATGTGAAGACGTTTGTGCGTGCTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgta-tgttctggctccg----------aagggttttggtctagttaaagtatcatt----atgtgttgcatatgattgcaagaattagaggtgtgaacagtggagcactataggt---------------------------------------------
 || |||||| | |||||| |||  ||  | |||||||| ||||| |||||||||||||| ||||||||| ||| ||| || ||||||||||| || || ||| | ||||    ||            |  ||| || |    |||  |||| |||    | |||||     | | |   | |  |  || | |   ||    | | || |   |                                             
AGTTTGGGCTCTGAGCAAGCACTTCCCAAACGTGAAGACTTTTGTCCGTGCTCATGATGTTGATCATGGATTGAATTTAGAAAAGGCTGGAGCTACCGCTgtaatattctattaccttttctattatgaatgttatgattgccttatggtataattttggaagtgtttttctttactaatacatatttagatttagccaaaata-ctctgttaatcttctctgtcttatctctttatctctctgcctcttgcatttgcag

upper sequence: PP1S2_217V6.1 (Physcomitrella patens), 5'ss of exon 20
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 16
GGTGTGGGCTTTAAGCAAGTACTATCCTCATGTGAAGACGTTTGTGCGTGCTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctggctccgaagggttttggtctagt-taaagtatcattatgtgttgcatatg-attgcaaga---attagaggtgtg-aacagtggagcactataggt-------------------------------------------------------------------------------------------
 || |||||  | |||||||| | |||  ||||||| || ||||| |||||||||||||| ||||||||  | | |||||| |||||||| ||||| |||||||  | |   |          ||  |||| | |  | | |  | |  | |||   ||  ||||||  |   |||  |  | |  |||     |     |||  |                                                                                           
TGTTTGGGCCCTGAGCAAGTATTTTCCCAATGTGAAAACATTTGTCCGTGCTCATGATGTTGATCATGGCCTTAATTTGGAAAAGGCTGGGGCAACAGCGgtatcat-taattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacag

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|162256773|gb|FC432667.1|FC432667
EST:     CTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCG                         GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
genomic: CTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctg ... atgattccagGTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
EST: gi|162178087|gb|FC354389.1|FC354389
EST:     CATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCG                         GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
genomic: CATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctg ... atgattccagGTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
EST: gi|162167759|gb|FC344073.1|FC344073
EST:     CTCNTGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCG                         GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
genomic: CTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctg ... atgattccagGTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
EST: gi|162174994|gb|FC350893.1|FC350893
EST:     GAGCAACTGCG                         GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
genomic: GAGCAACTGCGgtatgttctg ... atgattccagGTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
EST: gi|162174995|gb|FC350894.1|FC350894
EST:     CTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCG                         GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
genomic: CTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctg ... atgattccagGTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
EST: gi|162178086|gb|FC354388.1|FC354388
EST:     CATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCG                         GTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT
genomic: CATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctg ... atgattccagGTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTT

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: 31 (upstream exon), 33 (downstream exon)
Score: 3

GGTGTGGGCTTTAAGCAAGTACTATCCTCATGTGAAGACGTTTGTGCGTGCTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctg ... atgattccagGTCGTGCCAGAGACATTGGAGCCTAGTTTGCAGTTAGCAGCTGCTATTCTTGCTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTGGGCTTTAAGCAAGTACTATCCTCATGTGAAGACGTTTGTGCGTGCTCATGATGTGGATCATGGAATGAGTTTGGAGAAGGCTGGAGCAACTGCGgtatgttctggctccgaagggttttggtctagttaaagtatcattatgtgttgcatatgattgcaagaattagaggtgtgaacagtggagcactataggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA