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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgcgcacttaggttttaatctgggtgatgcatgttgggttcagaggtcttttagttaggagaatattgccctaattgttaccatgaaacccta...

Basic information

species Physcomitrella patens
transcript PP1S174_60V6.1
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|162260962|gb|FC438019.1|FC438019
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|208366209|gb|DC955308.1|DC955308
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|162235362|gb|FC412329.1|FC412329
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|7147644|gb|AW509566.1|AW509566
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCNCTCANGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|208391751|gb|DC942313.1|DC942313
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|208397933|gb|DC916688.1|DC916688
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|208348700|gb|DC926375.1|DC926375
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|208344646|gb|DC912592.1|DC912592
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|37834392|gb|BJ592404.1|BJ592404
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|67570006|gb|BJ942830.1|BJ942830
EST:     AGGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: AGGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|37831305|gb|BJ589317.1|BJ589317
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|18351976|gb|BJ184028.1|BJ184028
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|100441642|gb|BY962733.1|BY962733
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|6102404|gb|AW126874.1|AW126874
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGC
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGG-AGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGC
EST: gi|208377497|gb|DC902792.1|DC902792
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
EST: gi|162235361|gb|FC412328.1|FC412328
EST:     GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT                         GAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA
genomic: GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCA

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: 65

GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgc ... gcttttgcagGAAGGAGGAGGTGCACCCCCTCAGGGAAGCCTTTCTAAGGCCATTGATGCACAGTTTGGGGACCTGGACAAATTGATTGCAAAGATGAATGCTGCGGGCG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGTgtaagctcgcgcacttaggttttaatctgggtgatgcatgttgggttcagaggtcttttagttaggagaatattgccctaattgttaccatgaaacccta

- - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - GGAAGA