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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctttggctgagtttttctagtatattgccatttacttctcttctttgacaccgttgaccatcttgatattgggatatcggtgcttatgatagagtgtctcgtgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGTCACTGGAGAAGGCCTTGGAGCTGGTGGACATGTGTATTGAAGAAGTGAG

Basic information

species Physcomitrella patens
transcript PP1S50_46V6.1
intron # 2
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|208392638|gb|DC938575.1|DC938575
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208355347|gb|DC949841.1|DC949841
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|162272218|gb|FC448727.1|FC448727
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|100362522|gb|BY947396.1|BY947396
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|162272219|gb|FC448728.1|FC448728
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208371092|gb|DC955940.1|DC955940
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208369177|gb|DC936034.1|DC936034
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|162243419|gb|FC425115.1|FC425115
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208390808|gb|DC945867.1|DC945867
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208385896|gb|DC956734.1|DC956734
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|162228755|gb|FC405783.1|FC405783
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208353546|gb|DC918518.1|DC918518
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|162228756|gb|FC405784.1|FC405784
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208358786|gb|DC942952.1|DC942952
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|37841683|gb|BJ599691.1|BJ599691
EST:     CTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: CTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208364572|gb|DC935357.1|DC935357
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|18355750|gb|BJ187809.1|BJ187809
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|208366705|gb|DC931362.1|DC931362
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|37832695|gb|BJ590707.1|BJ590707
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
EST: gi|162243418|gb|FC425114.1|FC425114
EST:     GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACG                         GTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT
genomic: GGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGT

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), 34 (downstream exon)
Score: 10

ATGATGATAGCTGGGTGGGATAAGGACCAGGGTCCATCTCTTTACTACTTGGACTATATCTCAACCCTTCATAAGGTTGAGAAAGGTGGAATGGGTTACGgtaagttctt ... tgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGTCACTGGAGAAGGCCTTGGAGCTGGTGGACATGTGTATTGAAGAAGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatcttgatattgggatatcggtgcttatgatagagtgtctcgtgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGTCACTGGAGAAGGCCTTGGAGCTGGTGGACATGTGTATTGAAGAAGTGAG
    tcttgat  putative branch site (score: 10)
      ttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctttggctgagtttttctagtatattgccatttacttctcttctttgacaccgttgaccatcttgatattgggatatcggtgcttatgatagagtgtctcgtgtgatatagGTGCATACTTTCTGCTTTCACTCATGGACCGATACTATGAGAAGAACATGTCACTGGAGAAGGCCTTGGAGCTGGTGGACATGTGTATTGAAGAAGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT