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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCAGGCAGAGATTAATCAGTTGCTGAGTTTGATTATCAACACCTTCTACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatccatggaacttttttttccttatgcttggtcgcttgtctctgggttcctcgtcttctgtggcagttgtgtcatgctttgaatgcttccttcc...

Basic information

species Physcomitrella patens
transcript PP1S83_80V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_80V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA08G03690.1 (Glycine max), 5'ss of exon 1
-----------------CTTCCAGGCAGAGATTAATCAGTTGCTGAGTTTGATTATCAACACCTTCTACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatccatggaactt---ttttttccttatgcttggtcgcttgtctctgggttcctcgtcttctgtggcagttgtgtcatgctttgaatgcttccttcc
                  |||||| | ||||| || ||| | || ||| | || ||||||||||||||||||||||| || |||||| |  | ||| | ||||| ||  | || ||| |||| || | |  |   |    ||  |  ||||  |     | || ||  | | | |  |||    |   |    ||| |  ||      |||         
GAAACTGAGACGTTTGCTTTCCAGTCCGAGATCAACCAGCTCCTTAGTCTTATCATCAACACCTTCTACAGCAACAAGGAGATTTTCCTTAgtgagctcatcagcaatgcctctgatttaag-attcttatattatagggttcatgtttatcatactctgtttttccattgttgctccgtaacataacgtccctgtattgtgagaattatgtgggtag--

upper sequence: PP1S83_80V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv19s0015g01090.t01 (Vitis vinifera), 5'ss of exon 1
CTTCCAGGCAGAGATTAATCAGTTGCTGAGTTTGATTATCAACACCTTCTACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagt---atccatggaacttttttttccttatgcttggtcgcttgtctctgggttcctcgtcttctgtggcagttgtgtcatgctttgaatgcttccttcc
 |||||||| ||||| || ||  |  |||||||||| ||||||||||||||||||||||| || |||||  | || ||| | ||||| || || || |||||||||   || | |   |  |||||||        ||  ||  || | | |  |     |   ||   | || | ||     | || ||   | ||  |   
TTTCCAGGCTGAGATCAACCAACTCTTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTTCTCCGTGAGCTCATCAGCAATTCCTCTGATgtaagtcctatactttttatctttttttttcctcatttaatcagtttttttttcgcgatcctgttttatttgcggctgatctgttctctgttggtttatt---
















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|208392268|gb|DC949630.1|DC949630
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18329773|gb|BJ161779.1|BJ161779
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18332153|gb|BJ164166.1|BJ164166
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18349076|gb|BJ181125.1|BJ181125
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18354365|gb|BJ186421.1|BJ186421
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18362693|gb|BJ194764.1|BJ194764
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18329782|gb|BJ161788.1|BJ161788
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|208355223|gb|DC929740.1|DC929740
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18328074|gb|BJ160078.1|BJ160078
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18352175|gb|BJ184229.1|BJ184229
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18345152|gb|BJ177193.1|BJ177193
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18329734|gb|BJ161740.1|BJ161740
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|208392086|gb|DC941934.1|DC941934
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18342163|gb|BJ174198.1|BJ174198
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18353052|gb|BJ185107.1|BJ185107
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18347402|gb|BJ179448.1|BJ179448
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18325232|gb|BJ157228.1|BJ157228
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|208367220|gb|DC935824.1|DC935824
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18371697|gb|BJ203299.1|BJ203299
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
EST: gi|18352001|gb|BJ184053.1|BJ184053
EST:     ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGAT                         GCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT
genomic: ACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGAT

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), 24 (downstream exon)
Score: 5

CTTCCAGGCAGAGATTAATCAGTTGCTGAGTTTGATTATCAACACCTTCTACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatcc ... ttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGATGGCCAGCCAGAGCTCTTCATCCATATCATTCCCGACAAGGCGAACAATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCCAGGCAGAGATTAATCAGTTGCTGAGTTTGATTATCAACACCTTCTACAGCAACAAAGAAATTTTCTTACGAGAGTTGATCAGTAACTCATCCGATgtaagtatccatggaacttttttttccttatgcttggtcgcttgtctctgggttcctcgtcttctgtggcagttgtgtcatgctttgaatgcttccttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA