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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCCAGATGAGCTGTTCGAGGTGATCTCACAAGCTCTACTGGCGTCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttcaatttccgtttgatctcaagttagtgtttgtttggttgaatttcttgcgttttacataagcatcattgcaatttcaggtagcaatgtatcaaactggaaatgttgctcttgcag

Basic information

species Physcomitrella patens
transcript PP1S130_217V6.1
intron # 7
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|162247133|gb|FC421358.1|FC421358
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|18341730|gb|BJ173765.1|BJ173765
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|162206027|gb|FC382812.1|FC382812
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|162220662|gb|FC396874.1|FC396874
EST:     TTTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|67699719|gb|BJ959952.1|BJ959952
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|162213862|gb|FC389853.1|FC389853
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCCGGAC-AAGTTATTACCAAGACCTT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCC-GGACCAAGTTATTACCAAGACCTT
EST: gi|162243636|gb|FC421809.1|FC421809
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|37830057|gb|BJ588069.1|BJ588069
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|37821367|gb|BJ579433.1|BJ579433
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|162206028|gb|FC382813.1|FC382813
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTG
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTG
EST: gi|162213861|gb|FC389852.1|FC389852
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
EST: gi|162247132|gb|FC421357.1|FC421357
EST:     TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGT                         GACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT
genomic: TCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGT

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: 33 (upstream exon), 33 (downstream exon)
Score: 15

GGTCCAGATGAGCTGTTCGAGGTGATCTCACAAGCTCTACTGGCGTCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttc ... gctcttgcagGACTCCGGACCAAGTTATTACCAAGACCTTGAAGGGCCGCATGGATTGAGTTCTAACATCTTCTGAGATTTCAATGTGCCCCTGGTCGTTTTGTGGATCA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCCAGATGAGCTGTTCGAGGTGATCTCACAAGCTCTACTGGCGTCTGTGGACCGGGACTGCATTAGTGGATGGGGAGGGATTGTCCATGTTGTgtaagctttcaatttccgtttgatctcaagttagtgtttgtttggttgaatttcttgcgttttacataagcatcattgcaatttcaggtagcaatgtatcaaactggaaatgttgctcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA