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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAGGGCGTTCATGAAGGATCAGATTAAGCGAGCTCGCATGTTCTTCGTCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactcaatccataccactctatgtctccgattttctgaatatcaccaccacaaaaactctctctacacagaccctttaatctgatacacgcaatc...

Basic information

species Physcomitrella patens
transcript PP1S323_70V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ17751 (Selaginella moellendorffii), 5'ss of exon 5
GTGGAGGGCGTTCATGAAGGATCAGATTAAGCGAGCTCGCATGTTCTTCGTCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactcaatccataccactctatgtctccgattttctgaatatcaccaccacaaaaactctctctacacagaccctttaatctgatacacgcaatc
|||||| |||||||||||||| ||||| | | ||||||| |||||||||   ||||| |||| | | ||  ||||||| ||||| ||||| || ||||| || |||   ||   | |     | | |  || ||  |||||     |  | | | |  |   | |||   |   |   ||||  ||              
GTGGAGAGCGTTCATGAAGGACCAGATAACGAGAGCTCGGATGTTCTTCAAGGAGGCCGAGCTGGGTGTCATGGAGCTAGACAAAGACAGCCGGTGGCCTgtaagtcaacagcacgt-----tttctagcttcg-ctttctagcgctttcgatcgcttacgttttcta-gcgtgg---cttttttccag-----------
















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|162221128|gb|FC397769.1|FC397769
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37823421|gb|BJ581487.1|BJ581487
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162233127|gb|FC408950.1|FC408950
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162279508|gb|FC455819.1|FC455819
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37838421|gb|BJ596429.1|BJ596429
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162195317|gb|FC370838.1|FC370838
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162167422|gb|FC343125.1|FC343125
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37841215|gb|BJ599223.1|BJ599223
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|67578890|gb|BJ951057.1|BJ951057
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|67692313|gb|BJ952546.1|BJ952546
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162194278|gb|FC368500.1|FC368500
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162155565|gb|FC331009.1|FC331009
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162263002|gb|FC438810.1|FC438810
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37821980|gb|BJ580046.1|BJ580046
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|208347271|gb|DC917174.1|DC917174
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162213599|gb|FC389679.1|FC389679
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37838751|gb|BJ596759.1|BJ596759
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162178498|gb|FC354950.1|FC354950
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162196411|gb|FC373557.1|FC373557
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTTTTTTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37847253|gb|BJ605261.1|BJ605261
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37825130|gb|BJ583196.1|BJ583196
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162279509|gb|FC455820.1|FC455820
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37852048|gb|BJ610056.1|BJ610056
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162162257|gb|FC338039.1|FC338039
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|162220707|gb|FC395476.1|FC395476
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
EST: gi|37836953|gb|BJ594961.1|BJ594961
EST:     TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCA                         GTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG
genomic: TCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCG

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: 34 (upstream exon), 35 (downstream exon)
Score: 29

GTGGAGGGCGTTCATGAAGGATCAGATTAAGCGAGCTCGCATGTTCTTCGTCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactc ... taatgatcagGTATGGTCGGCTCTTCTATTGTACCAACAAATCCTGGACGCCATTGAAGCGAATGACTACGACAATTTCACAAAGAGAGCATACGTCAACAAGTGGAAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGAGGGCGTTCATGAAGGATCAGATTAAGCGAGCTCGCATGTTCTTCGTCGAGGCAGAGCAGAGCGTGCTGGAGCTCGACAAGGACAGTCGCTGGCCAgtgagtactcaatccataccactctatgtctccgattttctgaatatcaccaccacaaaaactctctctacacagaccctttaatctgatacacgcaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaaaaa