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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACCTGACCTCACGCCAGTCAGCACCCTCGAGATGCTAGAAGAAGCGTACACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcctttcaatcctcttcctctcagtcattggctccacgcaaccacagccatgcaagatatggccaaaaacagacaggaaccgcatatttctcgg...

Basic information

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

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|162195318|gb|FC370839.1|FC370839
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162194279|gb|FC368501.1|FC368501
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|100388426|gb|BY952028.1|BY952028
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGGACCCCTGAGAGGC
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATG-ACCCCTGAGAGGC
EST: gi|67507624|gb|BJ940505.1|BJ940505
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162183206|gb|FC360356.1|FC360356
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162196412|gb|FC373558.1|FC373558
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162213600|gb|FC389680.1|FC389680
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162263003|gb|FC438811.1|FC438811
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162167423|gb|FC343126.1|FC343126
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162221129|gb|FC397770.1|FC397770
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162178499|gb|FC354951.1|FC354951
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162279509|gb|FC455820.1|FC455820
EST:     CTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
EST: gi|162162258|gb|FC338040.1|FC338040
EST:     CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCG                         GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG
genomic: CACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG

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: 18

CGACCTGACCTCACGCCAGTCAGCACCCTCGAGATGCTAGAAGAAGCGTACACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcct ... ttatctacagGAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACCTGACCTCACGCCAGTCAGCACCCTCGAGATGCTAGAAGAAGCGTACACTCGCTGCGGCGAAGTCTGTGCTGAATACGCCAAAACGTTCTATCTCGgtaagttcctttcaatcctcttcctctcagtcattggctccacgcaaccacagccatgcaagatatggccaaaaacagacaggaaccgcatatttctcgg

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