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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatccttcaccttcattatgctaaaccctgtattatcgttacaccacacattttagcattttgataggcgtctctaattttcgccagcgtccgctctcaactttatggtgcatatctctctgactatgcatggtttggcatttgacag

Basic information

species Physcomitrella patens
transcript PP1S90_13V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S90_13V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA11G01670.1 (Glycine max), 5'ss of exon 11
-TGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatccttcaccttcattatgctaaacc---ctgtattatcgttac-accacacattttagcattttgataggcgtctctaattttcgccagcgtccgctctcaactttatggtgcatatctctctgactatgcatggtttggcatttgacag
 |   ||||  |   |   |   || |  ||  | | | ||||||||||| ||    || || || || |||||| ||||||||||||| ||||||||||||||   |  |  | |  |  || ||   ||| |   ||||| |||  | |  |  |      |||    |||| | |   |   |   || |  ||   |                                                          
CTTCCAGCTCTCCTGGTTCACAATCATCAAGCTTCTCA-TGGGTGTTTGACCTAAGGGGGATTGCAGAAATGTATCAATCCTATGAAGAAACAAATTTGTGgta--cttactgtgatatctatgataacaaagctagctgtaatatattgattattattggccttaattctttggttgagatgggttccttcctgcatgattg--------------------------------------------------------

upper sequence: PP1S90_13V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA01G44190.1 (Glycine max), 5'ss of exon 11
-TGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatccttcaccttcattatgctaaaccctgtattatcgttacaccacacattttagcattttgataggcgtctctaattttcgccagcgtccgctctcaactttatggtgcatatctctctgactatgcatggtttggcatttgacag
 |    |||  |   |   |   || |  ||  | | | ||||||||||| ||    || || || || |||||| ||||||||||||| ||||||||||||||   |  |  | |  |  || ||   ||      |  ||  | | ||  | | |||     ||||| || ||| |   |   ||| |      |  | ||    ||   | | |                                      
CTTCTGGCTCTCCTGGTTCACAATCATCAAGCTTCTCA-TGGGTGTTTGACCTAAGGGGGATTGCAGAAATGTATCAATCCTATGAAGAAACAAATTTGTGgta--cttactgtgatatctatgataacaa------tgcta--gctgca--atatattg----atttttatcggccttaatt-ctttggttgagatgggttccttcctgccttgagt-------------------------------------

upper sequence: PP1S90_13V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv18s0001g06010.t01 (Vitis vinifera), 5'ss of exon 11
-TGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatccttcaccttcattatgctaaaccctgtattatcgttacaccacacattttagcattttgataggcgtctctaattttcgccagcgtccgctctcaactttatggtgcatatctctctgactatgcatggtttggcatttgacag
     || | ||   |   |   |||   ||  | | | ||||||||||| ||  | || || ||||| |||||| ||||||||||||| |||||||| |||||  | ||  |      |  || | |   | | || |||   || | | | || |||     ||| |  ||       || ||||  |          ||   || || ||                                          
AGACCAGTTCCCCTGGTTCATCATCGCCAAGCTTCTCA-TGGGTGTTTGACCTCAAGGGAATTGCTGAGATGTATCAATCCTATGAAGAAACAAATTTATGgtat-tcatgttcagaacttgtttttc---atcttgaattgatgtcaaatctcatatt-----attcttctaaatacggcttatttctgaagat-----cttctaatttgataa----------------------------------------

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|162186441|gb|FC362997.1|FC362997
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|208396230|gb|DC924024.1|DC924024
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|162199310|gb|FC375146.1|FC375146
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|162240427|gb|FC419321.1|FC419321
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|162274410|gb|FC450645.1|FC450645
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|37836442|gb|BJ594450.1|BJ594450
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|22132775|gb|BQ827349.1|BQ827349
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|162190182|gb|FC365924.1|FC365924
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTA
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTA
EST: gi|162190181|gb|FC365923.1|FC365923
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|162162473|gb|FC339204.1|FC339204
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|162162472|gb|FC339203.1|FC339203
EST:     GGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: GGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|208367676|gb|DC947368.1|DC947368
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|162240428|gb|FC419322.1|FC419322
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
EST: gi|162186442|gb|FC362998.1|FC362998
EST:     CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTG                         GTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC
genomic: CTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGC

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: 32 (upstream exon), 33 (downstream exon)
Score: 42

TGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatc ... catttgacagGTCATTGGTGGACAACGTTCCAGAGGGGGTTCACATAGACTTTTTAAGAGCGGAGAGAAGTTTGCATCGTTGGGCCCACGAAGATGTGCAAAGGATTCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATGAAGATACAAATTTGTGgtagattatccttcaccttcattatgctaaaccctgtattatcgttacaccacacattttagcattttgataggcgtctctaattttcgccagcgtccgctctcaactttatggtgcatatctctctgactatgcatggtttggcatttgacag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA