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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagttcagctctggactggactgtttcttcgtttattcgggatttttctgtctgtttttaccatactggccactcgatcaccttcacattgctgt...

Basic information

species Physcomitrella patens
transcript PP1S47_221V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_221V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv13s0101g00100.t01 (Vitis vinifera), 5'ss of exon 2
AGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagttcagctc-tggactggactgtttcttcgtttattcgggatttttctgtctgtttttaccatactggccactcgatcaccttcacattgctgt-
|||||||| |||||||||||||||| || ||||| || || ||||| || |||||||| || |   | ||||  || || || || |||||  | || ||||| ||| | || | | |   || | |  ||| ||   ||||||    | || ||||   |||  | |   ||  ||   |       | | |   ||    
AGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTTAAGGACTATGCTTTAACCAGgta-ttattgcaacacatatgctaggc-atttatttacttattctatgtcttgctgtggttttgaatctctctctccctccccatctgtcccctacgccaaa
















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|162162945|gb|FC338142.1|FC338142
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|208358222|gb|DC939390.1|DC939390
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162227780|gb|FC402396.1|FC402396
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162197234|gb|FC372534.1|FC372534
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162251200|gb|FC428479.1|FC428479
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|100401256|gb|BY990911.1|BY990911
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|67696785|gb|BJ957018.1|BJ957018
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTNCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162227779|gb|FC402395.1|FC402395
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|100376173|gb|BY968329.1|BY968329
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162195536|gb|FC371837.1|FC371837
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162251201|gb|FC428480.1|FC428480
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162189471|gb|FC365485.1|FC365485
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162189470|gb|FC365484.1|FC365484
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162232574|gb|FC408917.1|FC408917
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|37828312|gb|BJ586324.1|BJ586324
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162229811|gb|FC404264.1|FC404264
EST:     CTTGAAGCCCGATATATCATCCCCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCACGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|100421718|gb|BY976278.1|BY976278
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCC
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCC
EST: gi|37821608|gb|BJ579674.1|BJ579674
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTNTCCGAGACCGCCGNTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162252999|gb|FC429060.1|FC429060
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|100435185|gb|BY979115.1|BY979115
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162156121|gb|FC332288.1|FC332288
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|18354817|gb|BJ186876.1|BJ186876
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTC
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTC
EST: gi|37844642|gb|BJ602650.1|BJ602650
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|67578357|gb|BJ950524.1|BJ950524
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|208360641|gb|DC957866.1|DC957866
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|7067000|gb|AW496855.1|AW496855
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|162253000|gb|FC429061.1|FC429061
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|7147954|gb|AW509876.1|AW509876
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCATGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|18351844|gb|BJ183896.1|BJ183896
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
EST: gi|67693517|gb|BJ953750.1|BJ953750
EST:     CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAG                         TGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA
genomic: CTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTA

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: 25

AGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagtt ... tattttgcagTGCTCTCCGAGACCGCCGCTTCCCTCCAATTCAGGCACGCGAGCTCCCTTACTTGGAATGCACGGTGTCACTCTTAACAGATTACGAAACCGCAGCTCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTCAAAGATTATGCGCTCACAAGgtagttagttcagctctggactggactgtttcttcgtttattcgggatttttctgtctgtttttaccatactggccactcgatcaccttcacattgctgt

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC