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

AGGGCTCTGTGCCAAGGTGGTGGTGGTTGACGCTCGTCACCATATGCTCGGCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactctgcctctgcaatgcgcgccttctcacatgttgtccgtttttttttttttttttttttttttttttccgtttctgtggaattctcggaatttaatgtagtcacctggggttgaatcag

Basic information

species Physcomitrella patens
transcript PP1S63_162V6.1
intron # 1
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|18353359|gb|BJ185414.1|BJ185414
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162244373|gb|FC421025.1|FC421025
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162205282|gb|FC380964.1|FC380964
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAAGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|208366844|gb|DC940158.1|DC940158
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162225076|gb|FC401700.1|FC401700
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162225077|gb|FC401701.1|FC401701
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|18342105|gb|BJ174140.1|BJ174140
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162209015|gb|FC385567.1|FC385567
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|67728015|gb|BJ978274.1|BJ978274
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGGGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162209016|gb|FC385568.1|FC385568
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|100368987|gb|BY984971.1|BY984971
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162207199|gb|FC382521.1|FC382521
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162225768|gb|FC400708.1|FC400708
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|18373903|gb|BJ205481.1|BJ205481
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|37821181|gb|BJ579247.1|BJ579247
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|208370695|gb|DC936845.1|DC936845
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|67726636|gb|BJ976895.1|BJ976895
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|18373813|gb|BJ205391.1|BJ205391
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162242094|gb|FC419428.1|FC419428
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|100442597|gb|BY963291.1|BY963291
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162205281|gb|FC380963.1|FC380963
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAACATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|67694236|gb|BJ954469.1|BJ954469
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162211930|gb|FC387802.1|FC387802
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|67718147|gb|BJ968406.1|BJ968406
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162220991|gb|FC396176.1|FC396176
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162220990|gb|FC396175.1|FC396175
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162242093|gb|FC419427.1|FC419427
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|67719750|gb|BJ970009.1|BJ970009
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGGGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|37847760|gb|BJ605768.1|BJ605768
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|208394042|gb|DC957123.1|DC957123
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|67570934|gb|BJ943758.1|BJ943758
EST:     GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
EST: gi|162225769|gb|FC400709.1|FC400709
EST:     GCCGATTGGCTTCCATTCTCACGAAAGAGCTTCTCAATGGCCAGAAAATC                         GTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG
genomic: GCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAG

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: 49

AGGGCTCTGTGCCAAGGTGGTGGTGGTTGACGCTCGTCACCATATGCTCGGCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactc ... gttgaatcagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAGAAGATGAAATACCTTAGGTTTTTGAGGAAGAGGATGAACACCAAGCCCA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGCTCTGTGCCAAGGTGGTGGTGGTTGACGCTCGTCACCATATGCTCGGCCGATTGGCTTCCATTCTCGCGAAAGAGCTTCTCAATGGCCAGAAAATCgtatgtactctgcctctgcaatgcgcgccttctcacatgttgtccgtttttttttttttttttttttttttttttccgtttctgtggaattctcggaatttaatgtagtcacctggggttgaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT