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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgcagttgggaggcagagacgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC

Basic information

species Physcomitrella patens
transcript PP1S348_15V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G36690.1 (Glycine max), 3'ss of exon 1
------gtttgcagt-tgggaggcagagacgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
       ||||     | | |   |     || | |   |||   || |    |||  | |||  |||     |||||    || |  ||||||| ||   | |||||||||||||| || |||||||| || ||||| || ||||| || ||||||||||||||||| ||| |||| ||||| || |||||||| |||||||| ||
tgttcaatttgtgacatcgtacttaagagtgttattcttgtttttcctgtgatgcgaggcttgatttg-----tgatgttttgtttt-tgcgttt-gtttgtggcagAGATGGTGGAATCAATGAAGAACGTTGCGAATCTCGACGTTGAACTGACGGTGGAGGAGCGGAATTTGCTTTCTGTTGGGTACAAGAATGTGATTGGTGC

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G33800.3 (Glycine max), 3'ss of exon 1
----gt-ttgcagttgggaggcagagacgtgagtgcggttgggcccggtgggcg-gcggttgtgttggtggatgatggagcgtgtggtgcgttttgtgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
    ||  ||||  |   ||     |    ||        |         |  | | || | | || |||     | ||   || |      |||||   | |||||||||||||| || |||||||| || ||||| || ||||| || ||||| ||||||||||| ||| | || ||||| || |||||||| |||||||| ||
tcgtgtgctgcatgttcaagttgtggtgccgaacttaagagattttatcagatgtgaggctttatttgtgatgttttgattttgcg------tttgtttgtggcagAGATGGTGGAATCAATGAAGAACGTTGCGAATCTCGACGTTGAACTGACTGTGGAGGAGCGGAATTTACTTTCTGTTGGGTACAAGAATGTGATTGGTGC

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G12220.5 (Glycine max), 3'ss of exon 1
----gtttgcagttgggaggcagagacgtgagtgcgg---ttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
    |||   |     ||      |  |||  |   |   |||  |   | ||    |  ||||||  |||  |  | ||| || ||||  ||| ||    ||  ||| ||||||||  | |||||||| |||||||||||  |||||||  ||||||| |||||||| || || ||||| || || |||||||||||| | || ||
tttggttcagacggttgaattttcgttgtggattttgaatttgaactttgcggagcacaattgtgt--gtgattttttgagtgtttggtatgttgtg---gtt--agAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTGAACGTGGAATTGACGGTCGAGGAGCGGAACCTTCTGTCGGTAGGGTACAAGAACGTGGTGGGTGC

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G29080.7 (Glycine max), 3'ss of exon 1
gtttgcagttgggaggcagagacgtgagtgcgg---ttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
 |||    || |  ||  ||    |   |  ||   |||     |     ||  |       | |||     |   | ||||  || || | |||  ||  ||| ||||||||  | |||||||| |||||||||||  |||||||  ||||||| |||||||| || || ||||| || || |||||||||||| | || ||
atttcggtttagacggttgaattttcgttttggattttgaatttgaatttcgcggagcacaattgtgagaatttttgagtgttttg-gtatggtg--ttttagAAATGGTGGAAGCAATGAAGAATGTGGCGAAGCTAAACGTGGAATTGACGGTAGAGGAGCGGAACCTTCTGTCGGTTGGGTACAAGAACGTGGTGGGTGC

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G22300.3 (Arabidopsis thaliana), 3'ss of exon 1
-gtttgcagttgggaggcagag-acgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtga-attgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
    ||  || |     |  || | |  | ||   | |  |   ||    ||  |     ||    |||   |||   | |  |    || ||||   |||||| ||||||||| ||||||||||||| ||  ||||||| |||||||| || ||||| ||| | |||||  | ||||| || |||||||| |||||||| ||
ttactgttgtcgaatctcttagcatgaaaatgaaatagatctacgtttttggaagcaa-attcaaagat--cggatattttttttttgttggtgatgatgcagAAATGGTGGAGGCGATGAAGAAAGTTGCTCAGCTTGATGTGGAGCTAACTGTGGAAGAGAGGAATCTTGTATCTGTAGGGTACAAGAATGTGATTGGTGC

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv19s0014g01420.t01 (Vitis vinifera), 3'ss of exon 1
gtttgcagttgggaggcagagacgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatgga-gcgtgtggtgcgttttgtgaat------tgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
||  |   || |      |         | | | ||       |  ||   || |  | |    |||  |    |  | |    | ||||| |||       |||||| ||||||||  |||||||||||||||||||||| || |||||  |||| ||||| ||||| ||| |||| || || || |||||||||||||| |||||
gtcagtgtttcgtccttcgctttccagat-ctgctgttttaatttcgctagggctagggtttcagattctaactggatttcactctttttgcgaaaattttgtgcagAAATGGTGGATGCGATGAAGAAAGTGGCGAAGCTGGATGTGGATTTGACTGTGGAAGAGCGGAATTTGCTTTCGGTTGGGTACAAGAACGTGATCGGAGC

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv10s0003g01240.t01 (Vitis vinifera), 3'ss of exon 1
---------------------gtttgcagttgggaggcagagacgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtgaattg-cagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
                     |||||  | |    |       |       | ||| |     | ||    |  || | |          || |   |    ||  |||| |   |||  ||| |||||||| || |||||||||||||||||||| ||||||||  |||| ||||||||||| || ||||| || || || |  ||||||||||| || ||
gtttccctctctctttctcctgtttgtggatctcggattaccccactctcactgttagagttag-ggtttccaattatctgatcactacctgaattttactctgtttttttttttttggtagAAATGGTGGATTCCATGAAGAAAGTGGCGAAGCTGGACGTGGAATTGACCGTGGAGGAGCGGAACCTGCTCTCGGTTGGCTTTAAGAACGTGATCGGCGC

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ36243 (Selaginella moellendorffii), 3'ss of exon 1
gtttgcagttgggaggcagagacgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtg-gtgcgttttgtgaatt-----gcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
                       |||||  |     ||  || || |      | | |     |     | |    |||| |||  | ||||  |||     ||||| ||||| || || |||||||| || || ||||| || |||||||| || |||||||| || ||||| ||||| ||||| ||||||||||| || || ||
-----------------------gtgagctc---ctggatcgatgcgataatctcgcgccttcgatccctcggatctgtgtgtgactcttgtctatttccccgcagAAATGGTCGAATCCATGAAGAAGGTCGCCAAGCTCGATGTGGAGCTCACCGTGGAGGAACGAAATCTCCTGTCCGTGGGGTACAAGAACGTTATCGGCGC

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ35972 (Selaginella moellendorffii), 3'ss of exon 1
gtttgcagttgggaggcagagacgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtg-gtgcgttttgtgaatt-----gcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC
                       |||||  |     ||  || || |      | | |     |  |  | |    |||| |||  | ||||  |||     ||||| ||||| || || |||||||| || || ||||| || |||||||| || ||||||||||| ||||| ||||| ||||| ||||||||||| || || ||
-----------------------gtgagctc---ctggatcgatgcgataatctcgcgccttcgattcctcggatctgtgcgtgactcttgtctatttccccgcagAAATGGTCGAATCCATGAAGAAGGTCGCCAAGCTCGATGTGGAGCTCACCGTGGAGGAGCGAAATCTCCTGTCCGTGGGGTACAAGAACGTTATCGGCGC

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|67717218|gb|BJ967477.1|BJ967477
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|208390694|gb|DC937850.1|DC937850
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGGCGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|208385562|gb|DC937107.1|DC937107
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|162270401|gb|FC447101.1|FC447101
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|67718418|gb|BJ968677.1|BJ968677
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|208370697|gb|DC936157.1|DC936157
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|67719261|gb|BJ969520.1|BJ969520
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|100373556|gb|BY948980.1|BY948980
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|208387877|gb|DC929221.1|DC929221
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|162269402|gb|FC445270.1|FC445270
EST:     GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
EST: gi|208354137|gb|DC957385.1|DC957385
EST:     GAGCGTTACGATG                         AGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG
genomic: GAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGG

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: 32 (upstream exon), 35 (downstream exon)
Score: 43

GCGTGTGGTGGTGCAGTTCGGGGCGACATGAGTACGGAGAAGGAGCGCGAGAGCTATGTGTATATGGCGAAACTCGCCGAGCAGGCGGAGCGTTACGATGgtgcgtgcat ... tgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcagttgggaggcagagacgtgagtgcggttgggcccggtgggcggcggttgtgttggtggatgatggagcgtgtggtgcgttttgtgaattgcagAGATGGTGGAGTCGATGAAGAAAGTGGCGAAGCTTGACGTGGAGCTGACGGTGGAGGAGCGCAATCTGCTGTCTGTGGGTTACAAGAACGTGATTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG