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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCGATTAACACTACCATACAAGTGGTGCGGGGTTTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttccattctttagtcatcaaagcattgatataaagcattgatatcgaagtaactcgtcactgcccttttctttttgtctatcctatgtggtattt...

Basic information

species Physcomitrella patens
transcript PP1S309_15V6.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S309_15V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT4G31480.2 (Arabidopsis thaliana), 5'ss of exon 5
GTGGCGATTAACACTACCATACAAGTGGTGCGGGGTTTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagt-tccattctttagtcatcaaagcattgatataaagcattgatatcgaagtaactcgtcactgcccttttctttttgtctatcctatgtggtattt
|| ||  | ||||| || ||||||   |   | |  ||| |  | || ||| |  | |||||||||||||| ||||||||| |||||||||| |  ||||||   |||||   | |   |   ||| |  |  |  | || |||  | ||  | |                                
GTTGCTGTGAACACCACAATACAAAACGAAAGAGAATTCCTCGACCACATTATCAAATCTACAAACATGAAATGTCTCACTGCTCCgtaagtgtaaattcttctttcatcct-gtagaaacgaaaaactcttcttactaattaatacttctttacttgcag--------------------------
















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|67697127|gb|BJ957360.1|BJ957360
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|162263080|gb|FC438836.1|FC438836
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|162171368|gb|FC346448.1|FC346448
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|67573739|gb|BJ946563.1|BJ946563
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|162259541|gb|FC435468.1|FC435468
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|67697126|gb|BJ957359.1|BJ957359
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|37844698|gb|BJ602706.1|BJ602706
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|37844411|gb|BJ602419.1|BJ602419
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|162165634|gb|FC341473.1|FC341473
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|67573738|gb|BJ946562.1|BJ946562
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|162174425|gb|FC350704.1|FC350704
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
EST: gi|162178785|gb|FC354002.1|FC354002
EST:     TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCC                         ATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA
genomic: TTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttcca ... gtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCGATTAACACTACCATACAAGTGGTGCGGGGTTTCTTGCAGCATATTGTTGATTCTACAAACATGAAGTGTCTCACTCCTCCgtaagttccattctttagtcatcaaagcattgatataaagcattgatatcgaagtaactcgtcactgcccttttctttttgtctatcctatgtggtattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC