Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACAGCTGATGAACAAACTGCGAAAAAGTTCGGACTTGACAAAAAGGCTCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaaatatatcctgaggatctctgagctttgacatatactgcttatgagcgagtttgataacgtgcggtgatacacttgaagatctaagttttttttttctcgaattggtgtatgagcag

Basic information

species Physcomitrella patens
transcript PP1S422_7V6.2
intron # 2
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|162228933|gb|FC404726.1|FC404726
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|162257578|gb|FC433712.1|FC433712
EST:     TCCTGCTCTCGTCTTGTTGAAGAAACAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGA
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGA
EST: gi|162166450|gb|FC342432.1|FC342432
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|162171848|gb|FC348985.1|FC348985
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|162218094|gb|FC394957.1|FC394957
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|100413810|gb|BY974995.1|BY974995
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|162170029|gb|FC345082.1|FC345082
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|162167529|gb|FC344220.1|FC344220
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|162248488|gb|FC420935.1|FC420935
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|67702577|gb|BJ962810.1|BJ962810
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|100419910|gb|BY975902.1|BY975902
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GGGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|162256673|gb|FC433191.1|FC433191
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|162249688|gb|FC426516.1|FC426516
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
EST: gi|100409294|gb|BY991940.1|BY991940
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAAAACAG
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACA-AG
EST: gi|162198843|gb|FC372870.1|FC372870
EST:     TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCG                         GTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC
genomic: TCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGC

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), 35 (downstream exon)
Score: 32

ATGACAGCTGATGAACAAACTGCGAAAAAGTTCGGACTTGACAAAAAGGCTCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaa ... gtatgagcagGTGGAGATTTTGAAAGAAAGGCTATTGGCGACTTTGTCTCGGAGAACAAGCTCCCTCTCGTTATTGTGTTTACTCGTGACACAGCCGAGATTATATTCGA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACAGCTGATGAACAAACTGCGAAAAAGTTCGGACTTGACAAAAAGGCTCCTGCTCTCGTCTTGTTGAAGAAGCAGAACGAGAAGGTTGCGACTTTCGgtacgtaaaaatatatcctgaggatctctgagctttgacatatactgcttatgagcgagtttgataacgtgcggtgatacacttgaagatctaagttttttttttctcgaattggtgtatgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC