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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttagaatgtgcacgcattcatattttgccgaactcaggtaacaagcttgctattgccaaaactcatagtgtcttattgtctttctccagtacatgaatgctactctaatacttcccggtgtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACACGATGACTTGGTAGATGAGATGAAGGGATTGGATGTGAATGAGGGTCCC

Basic information

species Physcomitrella patens
transcript PP1S243_63V6.1
intron # 22
splice site 3'
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|37851439|gb|BJ609447.1|BJ609447
EST:     CAGATTNGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CAGATT-GGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162157188|gb|FC332822.1|FC332822
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162168671|gb|FC343933.1|FC343933
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162239260|gb|FC416516.1|FC416516
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162239261|gb|FC416517.1|FC416517
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162149693|gb|FC326744.1|FC326744
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|37839801|gb|BJ597809.1|BJ597809
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162248787|gb|FC422014.1|FC422014
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162168672|gb|FC343934.1|FC343934
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAG
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAG
EST: gi|162174016|gb|FC350531.1|FC350531
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162248786|gb|FC422013.1|FC422013
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
EST: gi|162149694|gb|FC326745.1|FC326745
EST:     CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAG                         GACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA
genomic: CCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACA

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: 35 (upstream exon), 21 (downstream exon)
Score: 6

AAAGAGCAGCTGAATCACTAGCAGATCCACAAGAGTACCCCAATTTATTTCCAGATTGGGATTTGGCATGCGAGGCGGAAGTCCAGCACAGAGAACAGAGgtatgcttta ... gtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACACGATGACTTGGTAGATGAGATGAAGGGATTGGATGTGAATGAGGGTCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtctttctccagtacatgaatgctactctaatacttcccggtgtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACACGATGACTTGGTAGATGAGATGAAGGGATTGGATGTGAATGAGGGTCCC
                            ctctaat  putative branch site (score: 6)
                               taatactt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttagaatgtgcacgcattcatattttgccgaactcaggtaacaagcttgctattgccaaaactcatagtgtcttattgtctttctccagtacatgaatgctactctaatacttcccggtgtgtcgacagGACCAAGTTTCTTCTAGCCAAGGAGTATCTGAATTACATCAACGGTCAACACGATGACTTGGTAGATGAGATGAAGGGATTGGATGTGAATGAGGGTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG