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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcctctgaagacacttctttctttggacctctgtaccagtttacagtacgttgtttttaatgtactagaagtaaataaaattgaattgctttct...

Basic information

species Physcomitrella patens
transcript PP1S207_36V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 2
TCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcctctgaagacacttctttctttggacctctgtaccagtttacagtacgttgtttttaatgta-ctagaagtaaataaaattgaattgctttct
||| || || || ||||| |||||||||||||||||||||||  | ||||||||||||||||| ||||| || || |||  ||| || ||||| || ||||| |        ||      ||  || | |||     ||||  |  |     || |   || | |||  |   | ||     |       | | ||     
TCCAGTCACCGTATGTGGTGATATCCATGGCCAGTTTCATGATCTTATGAAGCTTTTTCAGACCGGAGGTCATGTTCCCGACACCAATTACATTTTTATGgtac-------cgag----ttttcttttgtggtgtcttgtatgacatattgatatgaaattatgaatacaatcataatctggtgtgggaaattcgcag---

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 2
TCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcctctgaagacacttctttctttggacctctgtaccagtttacagtacgttgtttttaatgtactagaagtaaataaaattgaattgctttct
||| || || || ||||| |||||||||||||||||||||||  | ||||| ||||| ||||| ||||| || || |||   || || ||||| || |||||    | ||||||         |    | | |   |  || || | |  |  || | ||||  ||| ||   |  |   ||    |             
TCCTGTCACCGTCTGTGGTGATATCCATGGCCAGTTTCATGATCTTATGAAACTTTTCCAGACCGGAGGTCATGTTCCCGAGACCAATTACATATTTATGgtata-gactctgactttgggcgtaggctcgtatgac-atatcaatatgtaacacatagttt--aat-tatctgtgggggattttctcag----------

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 2
TCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcctctgaagacacttc-----tttctttgg-acctctgtaccagtttacagtacgttgttttta--atgtactagaagtaaataaaattgaattgctttct---------
||| || ||||||||||| ||||| ||||||||||| |||||  | ||||| ||||| ||||| ||||| || || ||    || || ||||| || |||||  |    | |||   |  ||      || || |||  ||| | |  |   |    | |    | ||| |  ||  | |  |  |  || |  |||   | |||  |         
TCCAGTCACTGTTTGTGGTGATATTCATGGCCAGTTCCATGATCTAATGAAACTTTTCCAGACAGGAGGTCATGTACCAGAGACTAATTACATTTTTATGgtaag-atttatgattccgttttgagaattactatggtgcctttttgacttctctggggattcagatttcatcattcatttaatttctatgagcttgtcctccttaatacttggtag

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ05314 (Selaginella moellendorffii), 5'ss of exon 2
TCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtg----cgtgc-ctctgaagacacttctttctttggacctctgtaccagtttacagtacgttgtttttaatgtactagaagtaaataaaattgaattgctttct
||| || || || || |||||||| || |||||||| || || ||||||||||| || || ||||| || ||||||||   |||||| |||||||| |||||     || || || ||||   | || ||||||   || |   | ||| |     |  | |  |||  |                                   
TCCAGTGACAGTGTGCGGCGATATTCACGGCCAGTTCCACGATTTGATGAAGCTCTTCCATACTGGTGGGCACGTCCCTCACACAAATTACATCTTTATGgtaaaatcgagctctttgaatctagttgtttctt---acattgcttccatt-----gctcttcctttccag----------------------------------

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|208390402|gb|DC933447.1|DC933447
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|100389837|gb|BY971189.1|BY971189
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATT-ACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|100386396|gb|BY951192.1|BY951192
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|18356799|gb|BJ188858.1|BJ188858
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|162174230|gb|FC350613.1|FC350613
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAATTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|100381804|gb|BY950182.1|BY950182
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|208389011|gb|DC937344.1|DC937344
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|208390592|gb|DC937524.1|DC937524
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|100352556|gb|BY945331.1|BY945331
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|100353825|gb|BY983329.1|BY983329
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
EST: gi|208387516|gb|DC933379.1|DC933379
EST:     AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATG                         GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT
genomic: AGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTT

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: 28 (upstream exon), 32 (downstream exon)
Score: 4

TCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcct ... gaatgcgcagGGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGCTTTTTCAGACTGGAGGACACGTCCCCAGCACAAACTACATCTTCATGgtgcgtgcctctgaagacacttctttctttggacctctgtaccagtttacagtacgttgtttttaatgtactagaagtaaataaaattgaattgctttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaaa