Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatattacacttaccgacgggcttccccgtccattaaccttgtaaatacagtataatttattctggatttagatttgagacaatacgtttttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCGAAGAGACCAGAAACAGTGTCAGCAATTGATGGTGCATCCTTCGGTGTGG

Basic information

species Physcomitrella patens
transcript PP1S45_86V6.1
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|100362458|gb|BY947367.1|BY947367
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100425613|gb|BY958683.1|BY958683
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100437465|gb|BY979665.1|BY979665
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100422238|gb|BY957925.1|BY957925
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|162258364|gb|FC434915.1|FC434915
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100418702|gb|BY975699.1|BY975699
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100386765|gb|BY970306.1|BY970306
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|208391431|gb|DC937579.1|DC937579
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|208374474|gb|DC941203.1|DC941203
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100397599|gb|BY990307.1|BY990307
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|208390052|gb|DC938107.1|DC938107
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTANCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100392348|gb|BY953318.1|BY953318
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100360635|gb|BY984217.1|BY984217
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100356582|gb|BY965177.1|BY965177
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100430157|gb|BY978275.1|BY978275
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100441285|gb|BY962574.1|BY962574
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|18328811|gb|BJ160817.1|BJ160817
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCG
EST: gi|100443033|gb|BY981659.1|BY981659
EST:     TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGG                         AATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATTCAAA-CTACAGC
genomic: TGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAAT-CAAAACTACAGC

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-Seq library.


Block sizes: 33 (upstream exon), 35 (downstream exon)
Score: 18

GCACTGACATGGCAGGTGAAGTTGTTGGCCTTGGTCCTGGAGTGACATCTTTTGCTGTCGGCGACAAAGTATCCTGTTGGTCGGATATCCGGgtatgcaatt ... tttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCGAAGAGACCAGAAACAGTGTCAGCAATTGATGGTGCATCCTTCGGTGTGG































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacagtataatttattctggatttagatttgagacaatacgtttttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCGAAGAGACCAGAAACAGTGTCAGCAATTGATGGTGCATCCTTCGGTGTGG
                                           tttttgtccc  CT-rich tract
     agtataatttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatattacacttaccgacgggcttccccgtccattaaccttgtaaatacagtataatttattctggatttagatttgagacaatacgtttttgtcccagAATGGGGGATCATTAGCCGAGTACGCAGCAGTGCCAATCAAAACTACAGCGAAGAGACCAGAAACAGTGTCAGCAATTGATGGTGCATCCTTCGGTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA