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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctttcagtttcatcttgtagacacttaaatgctgaaagtttgatgtcatggtgaattgctagtgtagcttctaaattcggcaatctgaataatcctagtctcgtctttctttttttgtttctctgcttgctcttctctttgaaattatggttttattaacattgtttgttattggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCTGTACGAGTTGGTCAAGCTGTTGATGTGGTTGGTCAAGCTGGTCGCCCCA

Basic information

species Physcomitrella patens
transcript PP1S3_553V6.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S3_553V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 23
gtaaatctttcagtttcatcttgtagacacttaaatgctgaaagtttgatgtcatggtgaattgctagtgtagcttctaaattcggcaatctgaataatcctagtctcgtctttctttttttgtttctctgcttgctcttctctttgaaattatggttt--tattaacattg---tttgttattggatg-acagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCTGTACGAGTTGGTCAAGCTGTTGATGTGGTTGGTCAAGCTGGTCGCCCCA
                                                                                                       || | |||  |  ||  ||  ||  | | ||  | | ||  |  ||| ||   |||  || ||| ||||   | | || ||| ||| ||||||  | ||| |  ||||  |||||||  || |||| ||  |  ||||||| ||||| ||||| ||||||||||||||||||||||| |||||  | ||||
-------------------------------------------------------------------------------------------------------gtatggtccat--ttagttaattgacagttttgt-tgctagtgcaaactactatttggtactaaaattgagttctcttcttgtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA
















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|162280078|gb|FC456472.1|FC456472
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|37835828|gb|BJ593840.1|BJ593840
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|37848700|gb|BJ606708.1|BJ606708
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|162176023|gb|FC351024.1|FC351024
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|18336901|gb|BJ168924.1|BJ168924
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|162176009|gb|FC351023.1|FC351023
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|37830143|gb|BJ588155.1|BJ588155
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         TCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|37846451|gb|BJ604459.1|BJ604459
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|67578805|gb|BJ950972.1|BJ950972
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|37827765|gb|BJ585777.1|BJ585777
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|162163326|gb|FC339652.1|FC339652
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|18337499|gb|BJ169523.1|BJ169523
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|37839139|gb|BJ597147.1|BJ597147
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|37824468|gb|BJ582534.1|BJ582534
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|37826418|gb|BJ584430.1|BJ584430
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|67507537|gb|BJ940419.1|BJ940419
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
EST: gi|162186176|gb|FC362108.1|FC362108
EST:     TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAG                         CCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT
genomic: TTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCT

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: 23 (upstream exon), 13 (downstream exon)
Score: 2

GGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAAATCTTTCATTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTGGCAATGCAGgtaaatcttt ... tggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCTGTACGAGTTGGTCAAGCTGTTGATGTGGTTGGTCAAGCTGGTCGCCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcttctctttgaaattatggttttattaacattgtttgttattggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCTGTACGAGTTGGTCAAGCTGTTGATGTGGTTGGTCAAGCTGGTCGCCCCA
                          tattaac  putative branch site (score: 2)
                       ttttattaacattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctttcagtttcatcttgtagacacttaaatgctgaaagtttgatgtcatggtgaattgctagtgtagcttctaaattcggcaatctgaataatcctagtctcgtctttctttttttgtttctctgcttgctcttctctttgaaattatggttttattaacattgtttgttattggatgacagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCTGTACGAGTTGGTCAAGCTGTTGATGTGGTTGGTCAAGCTGGTCGCCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG