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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtccaatgctccagatcctcgttgctttcagaaggggtcatttgaaacggagtttcattcgaaaattctgaagtgtgcagtcgtgaacataattgatttggtggacatctctttgtttaggatacggtatgacttacaatggatgtcgataatggtgcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGATGCTGATCAATACGTCTTCATGGATATG

Basic information

species Physcomitrella patens
transcript PP1S49_243V6.1
intron # 3
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|208380630|gb|DC919388.1|DC919388
EST:     ACACAG-TGATCGTA-NTTCCGAGC-GGAGAGTCN                         GTTGATGAGGCCAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|7147836|gb|AW509758.1|AW509758
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208351044|gb|DC910507.1|DC910507
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208374301|gb|DC941142.1|DC941142
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|100388850|gb|BY988726.1|BY988726
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208350709|gb|DC918169.1|DC918169
EST:     ATCACTGGCAACACAGNTGATCGTAC-TTCCGAGC-GGAGAGTCG                         G-TGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208396719|gb|DC924331.1|DC924331
EST:     CACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: CACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|100362161|gb|BY947220.1|BY947220
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208348904|gb|DC921676.1|DC921676
EST:     ATCACTGGCNACACAG-TGATCGTACTTTCCGAGCNGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208348263|gb|DC905505.1|DC905505
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|67696624|gb|BJ956857.1|BJ956857
EST:     ACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208344391|gb|DC912750.1|DC912750
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208379070|gb|DC911595.1|DC911595
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|67573240|gb|BJ946064.1|BJ946064
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|162221894|gb|FC398162.1|FC398162
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208379038|gb|DC907787.1|DC907787
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208392456|gb|DC904274.1|DC904274
EST:     ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
EST: gi|208361708|gb|DC954142.1|DC954142
EST:     ATCACTGGCNACACAGNTGATCGTACTTTCCGAGCGGGAGAGTCG                         GTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT
genomic: ATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGAT

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), 31 (downstream exon)
Score: 3

GCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGCTGCGAAACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGGAGAGTCGgtatgtccaa ... gcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGATGCTGATCAATACGTCTTCATGGATATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttaggatacggtatgacttacaatggatgtcgataatggtgcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGATGCTGATCAATACGTCTTCATGGATATG
                   gacttac  putative branch site (score: 3)
                      ttacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtccaatgctccagatcctcgttgctttcagaaggggtcatttgaaacggagtttcattcgaaaattctgaagtgtgcagtcgtgaacataattgatttggtggacatctctttgtttaggatacggtatgacttacaatggatgtcgataatggtgcaacaacagGTTGATGAGGCAAGCATTTCCAAGGAAGTCAAGCAGTACACCTACATGGATGCTGATCAATACGTCTTCATGGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA