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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctgtctctatttgctatgatgctgctgttgcctgtatttattgataattaaatctctcttaatgatctattacatcctagattgagaacaccaca...

Basic information

species Physcomitrella patens
transcript PP1S262_27V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S262_27V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA17G34250.1 (Glycine max), 5'ss of exon 1
TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTG-ATAAGAACGAGAGgtctgctgtctctatttgctatgatgctgctgttgcctgtattta-ttgataattaaatct-ctcttaa-tgatctattacatcctagattgag-aacaccaca--
        || |||||||| |||||||||||||||||||||||||| ||| |||| ||||| ||||| || |  || ||| |||||| ||  ||    |  | | | |  || | ||   |   || |      |   ||  ||||  |||| ||||  | | ||||||| ||||  ||  |||   |  ||| |  | |       
-------AAAGGACTGGCTGTCTTTGGTTGCTGTGCACAGTGATGCTTGGTTGCTTGCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGACAGgtacctattttcctttctattcaatatgtatatgggtttaactgattattattttttctcttaaatgatgcat-gcatttgatcttgggcgatattgttaa

upper sequence: PP1S262_27V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA14G11400.3 (Glycine max), 5'ss of exon 2
TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTG------ATAAGAACGAGAGgtctgctgtctctatttgctatgatgctgctgttgcctgtatttattgataattaaatctctcttaa-tgatctattacatcctagattgagaacaccaca----
        || |||||||| |||||||||||||| ||||||||||| ||| |||| ||||| ||||| || |  || ||| ||||||      | |||   || ||||      | ||| ||  ||   ||     | | | ||    | |||  || ||   | |||||||| ||||  ||   ||  | ||||  |  ||  |      
------AAAAGGACTGGCTGTCTTTGGTTGCTGTACACAGTGATGCTTGGTTGCTTGCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattttcttttctcttcaatatgtatatggacttagctgattattattt---tttctcttaagtgatgcat-gtatttt-gattttgggcaatattgtta

upper sequence: PP1S262_27V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA16G00680.1 (Glycine max), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGC------TCGGTTTGATAAGAACGAGAGgtctgctgt-ctctatttgctatgatg--ctgctgttgcctgtatttattgataa------------ttaaatctctcttaa-tgatctat-tacatcctagattgagaacaccaca-----------------------------------------
        ||||||||||| ||||| |||||||| || |||||||| ||| |||| ||| |||| ||||| |  |||||      | ||||||||||    || |||| |    | ||||       |   |   |||  |||  ||  | ||  ||  ||            ||  |||   |||   |||| ||| ||  || | | || |   |    |                                          
------AAAAAGACTGGCTATCTTTAGTTGCTGTTCATAGTGATGCATGGTTGCTTGCTATTGCATTCTATTTTGGAGCCAGATTTGGGTTTGATAAAGCTGACAGgtatttcatactctgaccataaatcttatctgaagttaacttaagttggtggaaaatcacaaagcagttggatcctgcttgtctgatttatgtatctcattggtttacttcttttcttcacgtgtctcattctctcttgatttgaatatgtaatgcag

upper sequence: PP1S262_27V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA09G07970.1 (Glycine max), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGC------TCGGTTTGATAAGAACGAGAGgtctgctgtctctatttgctatgatgctgctgttgcctgtatttattgataattaaatctctcttaatgatctattacatcctagattgagaacaccaca--------
        || |||||||| ||||| |||||||| ||||||||||| ||||| |   | || ||||||||||  || ||      | | ||||||||    || |||| |  |   ||| ||  | |      |  | |  | | || |   ||       |||   |     || || || | | | |   ||||   ||   ||        
------AAAAGGACTGGCTATCTTTAGTTGCTGTACACAGTGATGCATGGCTACAATCAGTGGCTTTCTACTTTGGGGCAAGATTTGGTTTTGATAAAGCTGACAGgtataatagttcttttctccaatcctttattat--cttatactctctgg------aattgtttcaggtgttcaatgagaacatgttttgaatgcatgccattgccttt

upper sequence: PP1S262_27V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA13G16740.1 (Glycine max), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTG------ATAAGAACGAGAGgtctgctgtctctatttgctatgatgctgctgttgcctgtatttattgataattaaatctctcttaatgatctattacatcctagattgagaacaccaca---
       ||| |||||||| ||||||||||| || ||||||||||| ||| | || || || ||||||||||  || || || ||||      ||||    || |||| || |     | | |       |  ||   ||   | |    ||||||   ||  |    |      || | |   || |    ||  |     ||     
------ATAAGGACTGGCTGTCTTTGGTTGCCGTTCACAGTGATGCATGGTTACTTGCAGTGGCTTTCTACTTTGGGGCACGATTTGGTTTTGATAAAGCTGACAGgtatgattctgttttctaactctttattgtgtttttttcttgcaattgatctctaggttggacagggaaatttttcggatgcc---tttcgtttttcatttac

upper sequence: PP1S262_27V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G26210.1 (Arabidopsis thaliana), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTT------TGATAAGAACGAGAGgtctgc-tgtctctatttgctatgatgctgctgtt-----gcctgtatttattgataat---------taaatctctc------ttaatgatctattacatcctagattgagaacaccaca------------------------------
        || || ||| | ||  | |||||||| ||||||||||| ||||| || |||||||||||||  |  |||||  ||||      ||| ||    || |||| ||  | ||  | |   || | |  ||  | ||       || | ||  ||| |  |          ||  |||||      | | || |||| | | ||   | ||  | |   | |                               
------AAAAGGATTGGTTGTCCCTTGTTGCTGTCCACAGTGATGCTTGGCTTCTTGCTGTTGCTTTCTTTTTTGGAGCCAGGTTTGGATTTGACAAAGCTGATAGgtatgtatatccttctcctctttaagtctaatcttcttacatctatgttccttggtggtatatagatgcaagcctctcagtcactcattgttctactccttcaccgtttatgtagctctctgtgatttatgttctttcacatttgttacag

upper sequence: PP1S262_27V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv12s0035g01980.t01 (Vitis vinifera), 5'ss of exon 3
TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGCTC------GGTTTGATAAGAACGAGAGgtc-tgctgtctctatttgctatgatgctgctgttgcctgtatt--tattgataattaaatctctcttaatgatctattacatcctag-attgagaacaccaca
        ||||||||| | ||  |||||||||||||||||||| | ||| |||| |||||||| ||||| |  || || |      |||||| |||||  || ||||    || | |  |  | |  |||  ||  |  || || | |   | |  |   | |||| | | ||  |||   ||        || ||    |   |    
------AGAAAGACTGGTTATCACTGGTTGCTGTGCACAGTGATTCATGGTTGCTTGCTGTTGCATTCTATTTTGGTGCCCGCTTTGGGTTTGGTAAGAGTGAAAGgtaacactttttggaacttcactgaaact-ttcctgtctttctcaatgtcaaatttcaaatgtttttttgtgagtcatggtggtgaagtatctccagttct---

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|208369927|gb|DC931504.1|DC931504
EST:     CTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTGATAAGAACNAGAG                         GAAGCGTCTTTTTANTATGGTAAACNAGCTCCCAACTGTATTTGACGTAAT
genomic: CTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctgtc ... gctctcacagGAAGCGTCTTTTTAATATGGTAAACGAGCTCCCAACTGTATTTGACGTAGT
EST: gi|100436873|gb|BY979568.1|BY979568
EST:     CTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTGATAAGAACGAGAG                         GAAGCGTCTTT
genomic: CTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctgtc ... gctctcacagGAAGCGTCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGCGTAAAGACTGGCTTTCTTTGGTTGCTGTGCACAGTGATGCCTGGCTGCTCGCTGTTGCTTTCTACTACGGAGCTCGGTTTGATAAGAACGAGAGgtctgctgtctctatttgctatgatgctgctgttgcctgtatttattgataattaaatctctcttaatgatctattacatcctagattgagaacaccaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC