Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGCTGCCTCGAAATCCTCTGAAGACCTATGATCCTCAGAACATTGATCCCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacacttccaatggtagttatgattctactatatttgtgcagtaaattatcatttgttatccatgtgaacgatatgtaatgatttgattgtttttagtgcag

Basic information

species Physcomitrella patens
transcript PP1S42_224V6.1
intron # 3
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|208388468|gb|DC953132.1|DC953132
EST:     AGGTGGAGTAGTGGACCGACCCAGTGGNCAG                         AAGGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTNCCTCCCCCCTAAG
genomic: AGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAA-GGGAAAAGAGCCATATGTGTCTGACTTGGACCTT-CCT-CCCCCTAAG
EST: gi|208396847|gb|DC924375.1|DC924375
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|162225957|gb|FC400975.1|FC400975
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|208354546|gb|DC918656.1|DC918656
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|18338000|gb|BJ170024.1|BJ170024
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|15728403|gb|BI740770.1|BI740770
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|162225958|gb|FC400976.1|FC400976
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|162201898|gb|FC376896.1|FC376896
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|208364166|gb|DC943422.1|DC943422
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAANAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|162241274|gb|FC416905.1|FC416905
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG
EST: gi|100410651|gb|BY992202.1|BY992202
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAATGAACCGACCCAGTGGACCG                         AAGGGAAAAGA
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGA
EST: gi|208351239|gb|DC921546.1|DC921546
EST:     CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAG                         AAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCNTAAGAAG
genomic: CCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAG

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: 33 (upstream exon), 32 (downstream exon)
Score: 14

TGGGCTGCCTCGAAATCCTCTGAAGACCTATGATCCTCAGAACATTGATCCCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacact ... tttagtgcagAAGGGAAAAGAGCCATATGTGTCTGACTTGGACCTTCCTCCCCCTAAGAAGTAGACAACACTAACTAGCCGAAAACCCCAGAGCTCGAATCTTGAGGTTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGCTGCCTCGAAATCCTCTGAAGACCTATGATCCTCAGAACATTGATCCCCTAACAACCTTCACGCGAGGTGGAGTAGTGGACCGACCCAGTGGACAGgtatgacacttccaatggtagttatgattctactatatttgtgcagtaaattatcatttgttatccatgtgaacgatatgtaatgatttgattgtttttagtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA