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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa...

Basic information

species Physcomitrella patens
transcript PP1S157_50V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g69080.1 (Oryza sativa), 5'ss of exon 2
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgt-atctacgcaaattaaattgcgtacggaagttcgaa--
| | || || ||||| |||||||| ||  | ||| | || ||  | ||||||||||||||||| |||||||||||||||||  | ||||| ||||| ||||||| |       |   |  | |    |     | |      | ||    |      |  | ||| ||  | | |  ||      |   |    |||      
CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttttcttccgcttctttgctagcctagctat--atttaactgattattttgaaattgtcattcatg-agtttttccctcaagcaattgttttcctc

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os04g31070.1 (Oryza sativa), 5'ss of exon 2
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgt---tttcaccctaaaaa-attatgatgctcgctgaatgtgtctgcca-gctactgtatctacgcaaattaaattgcgtacggaagttcgaa
| | || || || || || || |||||| ||||| | || || || || ||||||| |||||| ||||||||||| || ||| ||||||| |||||||||||||||    || |   |||   | | |  | |||||  | ||   |   |  || | | | |||| |||   ||  |   |||   |   ||   | ||     
CAGGCATGGTGATCTTCTTAATAAGTACATGTACCTTACTGGACGTGTTGACATGAAACAAATTGAGAAGACAATACAATACCTGATTGGGTCTGGGATGgtaagagctaatatctatttaggcatgatgatattattttcctttttacttaagtttacaatgctattgtggataaccttgtta---tcaatagccatgtctc--

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G180399_T01 (Zea mays), 5'ss of exon 2
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaag--ccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaat-taaattgcgtacggaagttcgaa-
| | || || || || || ||||||||| ||||| | || ||| | || || ||||| ||||| |||||||||||||||||  | ||||| ||||| ||||||| |    |  | |||| | ||    |  || |  | |    | ||  || |       |  ||||  | |     | | || ||  ||     | | |   
CAGGCATGGTGATCTTCTCAACAAGTACATGTACCTCACTGGGAGGGTAGATATGAGGCAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacatattctctctttttatcc----attttttcttacctatttaacatggcaagtctttcttgtacattcatgcttctgaagtgtttattttcggttgctt

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G32850.1 (Glycine max), 5'ss of exon 2
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgt-acggaagttcgaa------
| | ||||| || || || ||||| ||  |||||||||  || ||||| ||||||| |||||| |||||||||||||||||| | ||||| |||||||||||||||  | ||      ||  ||    ||| || |  ||    | |||   |      || || ||| || ||| |||      || |  |||  ||         
CAGACACGGTGATCTTCTTAACAAATATCTGTACTTGAGTGGACGAGTTGACATGAAACAAATTGAGAAGACAATTCAGTACCTTATTGGGTCTGGGATGgtaagatcctataca---actgtagtctattttggtcttctgctattgtagtttt--attaatgaatc-acacaa-ttatgcaatgtcaaagaaactcttgctaccc

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA02G15600.1 (Glycine max), 5'ss of exon 2
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgt-acggaagttcgaa------
| | ||||| || || || ||||| ||  | |||||||  || ||||| ||||||| |||||| || ||||||||||||||| | ||||| ||||| |||||||||  | ||      ||  ||    ||| || |  ||    |  ||   |      || || ||| || ||| | |      || |  |||  ||         
CAGACACGGTGATCTTCTTAACAAATATCTTTACTTGAGTGGTCGAGTTGACATGAAACAAATTGAAAAGACAATTCAGTACCTTATTGGGTCTGGAATGgtaagatcctataca---actgtagtctattttggtcttccgcaatggtagtttt--attaatgaatc-acacaa-tcatgcaatgtcaaagaaactcttgctaccc

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv05s0094g00750.t01 (Vitis vinifera), 5'ss of exon 2
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagt--tcgaa----
| | || || ||||| || ||||||||| | ||  || | || ||||| |||||||||||||| |||||||||||||| || ||||||||||| || ||||||||   |      |  ||  |  |||  | | ||        | |   |    ||| ||    | ||  |||||     |    |  |||| |  | | |    
CAGGCATGGTGACCTTCTCAACAAGTACCTATATCTGTCTGGACGAGTAGACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttccttcacatgaacatttgaaaggttttatctcta--aactactttaagcagtta----aactttgcaaaacttttgaaatgaggaaatgatgggaggct

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv05s0094g00580.t01 (Vitis vinifera), 5'ss of exon 2
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaatt--gcgtacggaagttcgaa---
| | ||||| ||||| || || |||||  | ||  || | ||  |||| ||||||| ||||||||||||||| |||||||| ||||||||  |||| ||||| |||  |    |     |  |      || |  |  |  ||| |        | | || |  ||  |    || | || ||   | |    |  ||   |   
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgctttttttttttttttttttttctgtagtcaatcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv05s0094g00550.t01 (Vitis vinifera), 5'ss of exon 1
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgcca--gctactgtatctacgcaaattaaattgcgtacggaagttcgaa-
| |  |||| ||||| || || |||||  | ||  || | ||  |||| ||||||| ||||||||||||||| |||||||| ||||||||  |||| ||||| |||  |    |     ||||      || |  |    |  |   ||  |   |    ||| |   |  || ||| ||    | | | |     |||  | 
CAGGGACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgcccttttttttttttttttctgtagtcagtcacaatcttcactagttcttgaactcaagttcttcttc-tccatcttttcatag

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca-tgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa
 ||||| || ||  |||| ||||||||  | ||| | || || ||||| |||||||  |||||||||||||| || ||||||||||| || ||||| |||||||||    | | | |||   ||    || |   | |   | |       |||  |||                                          
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcagagtttcttctttctcgggaactcaaaagtcggtttttccattcttgcag------------------------------------------

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ20424 (Selaginella moellendorffii), 5'ss of exon 1
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca---tgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgc-cagctactgtatctacgcaaat-taaattgcgtacggaagttcgaa
 || || || ||  |||| ||||||||  | |||   || || ||||| |||||||  |||||||||||||| || ||||||||||| || ||||| |||||||  |||||   | | |||   ||    || |   | | |||     |   ||    |||   |   | | |  || |  |    | | |    | ||     
TCGCCATGGTGATTTGCTCAACAAGTATCTCTACCGCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaaagagccagagtttcttctttctcgggaactcaaaagttcgggttttccatccttgcagggccgagaacaatccatacctcgggttcatctacacgt-----

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ20423 (Selaginella moellendorffii), 5'ss of exon 5
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca---tgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgc-cagctactgtatctacgcaaattaaattgcgtacggaagttcgaa
 || || || ||  |||| ||||||||  | |||   || || ||||| |||||||  |||||||||||||| || ||||||||||| || ||||| |||||||  |||||   | | |||   ||    || |   | | |||     |   |||   |||                                          
TCGCCATGGTGATGTGCTCAACAAGTATCTCTACCGCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaaagagccagagtttcttctttctcgggaactcaaaagttcgggttttccatctttgcag------------------------------------------

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ28408 (Selaginella moellendorffii), 5'ss of exon 1
----------------------CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca---tgttttcaccctaaaaaattatgatgctcgc-tgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa-----------
                       || || || ||  |||| ||||||||  | |||   || || ||||| |||||||  |||||||||||||| || ||||||||||| || ||||| |||||||  |||||   | | |||   || |  || |   | | |||| |     |   |||  | | ||    |   | | | |  ||  |    |   ||    |           
GTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAGTATCTCTACCGCACTGGACGAGTTGACATGAAGCAAATCGAGAAGACGATCCAgtacttgatcggttctggaatggtaaagagccagagtttcttctttctcaggaactccaaagttcgcgtttccatccttgcaggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccag

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ20425 (Selaginella moellendorffii), 5'ss of exon 4
----------------------------------------------------------------------------CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca---tgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgc-cagctactgtatctacgcaaattaaattgcgtacggaagttcgaa
                                                                             || || || ||  |||| ||||||||  | |||   || || ||||| |||||||  |||||||||||||| || ||||||||||| || ||||| |||||||  |||||   | | |||   ||    || |   | | |||     |   |||   |||                                          
ACTCTCGATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTCCGTGGGCAGTGGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATGTGCTCAACAAgtatctctaccgcactggacgagtcgacatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagagccagagtttcttctttctcgggaactcaaaagttcgggttttccatctttgcag------------------------------------------

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca---tgttttcaccctaaaaaattatgatgctcgctgaatgtgt-ctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa
 || || || ||  | || ||||||||  | ||| | || || ||||| |||||||  |||||||||||||| || ||||||||||| || ||||| |||||||||  |||   | | |||   ||    || |   | | ||| |   |   | || ||||                                          
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcgggaactcaaaagttcggtttttccattcttccag------------------------------------------

upper sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ22568 (Selaginella moellendorffii), 5'ss of exon 1
----------------------------------------------------------------------------CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca---tgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa
                                                                             || || || ||  |||| ||||||||  | ||  | || || ||||| || ||||  |||||||||||||| || ||||||||||| || ||||| |||||||  |||||   | | |||   ||    || |   | | |||  |  | |   | |  ||                                         
ATGGCACCCGCGACGAGACCGGTGCGAGCCCGAGTGCGTGGGCACTGTGGGGGCGTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAgtatctctagctcactggacgagtcgatatgaagcaaatcgagaagacgatccagtacttgatcggttctggaatggtaaagagccagagtttcttctttctcgggaactcaaaagttcg--ggttttccatccttgcag---------------------------------------

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|67725306|gb|BJ975565.1|BJ975565
EST:     ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATG                         GATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
genomic: ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcc ... ggctctgcagGATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
EST: gi|208366965|gb|DC951452.1|DC951452
EST:     ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATG                         GGTCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
genomic: ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcc ... ggctctgcagGATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
EST: gi|208389551|gb|DC945803.1|DC945803
EST:     ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATG                         GATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
genomic: ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcc ... ggctctgcagGATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
EST: gi|208389175|gb|DC945751.1|DC945751
EST:     ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATG                         GATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
genomic: ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcc ... ggctctgcagGATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
EST: gi|162273047|gb|FC449178.1|FC449178
EST:     ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATG                         GATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
genomic: ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcc ... ggctctgcagGATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
EST: gi|208370935|gb|DC944310.1|DC944310
EST:     ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATG                         GATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC
genomic: ACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcc ... ggctctgcagGATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTC

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), 35 (downstream exon)
Score: 36

CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcc ... ggctctgcagGATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTCCAGGAGAGGGCAACTTTCATTTCGCACGGTAACACTGCCCGTCATGCGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagccatgttttcaccctaaaaaattatgatgctcgctgaatgtgtctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaaaaa