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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 6
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT
                                                          | ||| |    |   |  ||| || ||   |     | ||| |  ||  |    || |  |    |||  | |||    |  | | | |   ||   |||||||||||| || ||||| | ||||||||| || || ||||||| |||||| |||||||| ||||| |||||||| || |||||||| |||||||||  |
----------------------------------------------------------gtaatttctcttgttgacagcggaatgcctttctcaaattttgtgtgtct----ttctcaaaatgcaacacacctg---aggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGGACTGGACAAATCAAAGAAGTTGAACGTGTAACCAGAGAGTCAAACTTCTATGAT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT----
                                                       |  | ||| |    | | |  ||| || ||   |     | ||| |  ||  |    || |  |    |||  | |||    |  | | | |   ||   |||||||||||| || ||||| | ||||||||| || || |||||||  ||||| |||||||| ||||| |||| ||| || |||||||| ||||| |||  |    
-------------------------------------------------------caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtct----ttctcaaaatgcaacacacctg---aggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GRMZM2G102756_T01 (Zea mays), 3'ss of exon 4
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT
                                                          | ||| |    | | |  ||| || ||   |     | ||    |||| ||   || |  |    |||  | |||    |  | | | |   ||   |||||||||||| || ||||| | ||||||||| || || |||||||| | ||| |||||||| ||||| |||| ||| || |||||||| ||||| |||  |
----------------------------------------------------------gtaatttctcttgctgacagcggaatgcctttctcaaatt----atgcgtgtctttctcaaaatgcaacacacctg---aggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAAAATTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGAT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgc--atgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT
                               |  || ||| | ||  ||      ||||   |   ||    |||||      | || |   |||| |   |    ||| | || |||  ||| |   ||| |  | |||          | ||   ||| ||||| ||||| || ||||  |||||||||||||| |||||||||||||| ||||||||||| || || ||||| |||||||| || || ||||||  |
------------------------------gtaattctttcatttggaaaaaaaacttgtttttctgt---tggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataa----------tatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgc--atgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT
                         |  |  |||  |||  ||    ||  |||  ||    |||| |    |||||      | || |   |||| |        ||| | || |||  ||| |   ||| |  | |||          | ||   ||| ||||| ||||| || ||||  |||||||||||||| || ||||||||||| ||||||||||| || || ||||| |||||||| || || ||||||  |
------------------------gtaattctttcatttggaaaaaaaaacttgtttt----tctgtt----ggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataa----------tatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
gtgggaatttatgtcttttctttctttctgtt-tttttttttaattttaattttggcttggaatctggtatacg-gtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT
                             ||   | |||  |  |||||    ||  ||||   |||||  ||  || |    |||  ||  || ||  |||      || |  | ||   |      |   ||   | ||||         || | ||| ||||| ||||| || |||| ||||||||||||||| |||||||||||||| |||||||| || || || ||||| || ||||| || |  || |||  |
-----------------------------gtaactctttcatgtttttagaactgttttgg---ctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatattt------ttttccc--tgaact---------tgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaag-ttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT
                                                                || |||| | |||  |   |||| | | |    |    | ||| ||   || |   |  |   |     |   ||  | | ||| | || |  || ||||| ||||||||||| | |||||||||||| || || || |||||||| ||||| ||||| || || ||||| || |||||||| |||||||||  |
---------------------------------------------------------------gtgatata-gataa--aatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT
                                                                  ||||    |      |  || |    ||| |||    |  |  |  || || ||     ||   | || |   |    || ||||| | ||||||||||||||| ||||||| ||| ||||||||||| || || || ||||| ||||| ||||| || |||||||| ||  | || || ||||| |||  |
------------------------------------------------------------------gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtat-----attttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT

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), 18 (downstream exon)
Score: 5

ATGGGGAACAGCTGGGTGTTGATTCTTGTGTAAAGTTGTTTGAGAGCTTCAAATCATACGAAGGCCTTTACTTCTTCCTTGGCGCATACTTAAGTACAAGgtgggaattt ... tttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT
                                       tatcttttt  CT-rich tract
                                taaactatatcttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA