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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACACTATCTGGGTCCAGAATGGAAACGATGACTACGATGCTATCCGAGCTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaacagctttttatttatctacttttttaatatcttccgaatatcagcatcagatttctgttacttgtttattagtttctacatttcatgttgggttgctgcatgaacttgtatttgctgatattcttgaatcatgaaatttag

Basic information

species Physcomitrella patens
transcript PP1S72_25V6.1
intron # 4
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|162187677|gb|FC364628.1|FC364628
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162166276|gb|FC342869.1|FC342869
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162258554|gb|FC434769.1|FC434769
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162162334|gb|FC339130.1|FC339130
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162151356|gb|FC327485.1|FC327485
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162173575|gb|FC350149.1|FC350149
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162155491|gb|FC330974.1|FC330974
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162154792|gb|FC331106.1|FC331106
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162153909|gb|FC329416.1|FC329416
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162157000|gb|FC333362.1|FC333362
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162186385|gb|FC362941.1|FC362941
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162160705|gb|FC337228.1|FC337228
EST:     GGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: GGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162193953|gb|FC371766.1|FC371766
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162166482|gb|FC343179.1|FC343179
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162195116|gb|FC368804.1|FC368804
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162248959|gb|FC421458.1|FC421458
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162160911|gb|FC337468.1|FC337468
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162193760|gb|FC368700.1|FC368700
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162174042|gb|FC350557.1|FC350557
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162180307|gb|FC355312.1|FC355312
EST:     CAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162190600|gb|FC366238.1|FC366238
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|67716179|gb|BJ966439.1|BJ966439
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162254948|gb|FC431133.1|FC431133
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162176957|gb|FC353634.1|FC353634
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162161260|gb|FC337323.1|FC337323
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162255769|gb|FC431429.1|FC431429
EST:     TGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAAATGATCA-G                         GTGACAACCACAATCGGATATGGTTCA
genomic: TGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAA-TGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCA
EST: gi|162177841|gb|FC355091.1|FC355091
EST:     CCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162173510|gb|FC350084.1|FC350084
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
EST: gi|162167290|gb|FC342278.1|FC342278
EST:     CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAG                         GTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT
genomic: CTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCT

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), 34 (downstream exon)
Score: 98

GCACACTATCTGGGTCCAGAATGGAAACGATGACTACGATGCTATCCGAGCTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaa ... tgaaatttagGTGACAACCACAATCGGATATGGTTCACCAAACAAGGCCAACTCATACGCTGTGCATGGTGCCGCTCTGGGAACAAAAGAAGTAGATGCAACCCGCCAAA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACACTATCTGGGTCCAGAATGGAAACGATGACTACGATGCTATCCGAGCTGCCATCGAGGAGGCGAAGTCAGTAACTGATAAGCCCACAATGATCAAGgtacacttaacagctttttatttatctacttttttaatatcttccgaatatcagcatcagatttctgttacttgtttattagtttctacatttcatgttgggttgctgcatgaacttgtatttgctgatattcttgaatcatgaaatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG