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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCCCACTGGTGTTGACCCGACTGAAGAGCAGTGGGAAGGGATTCGACAGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgttactattggattcaattttggtcatttctcactttatttttttattattttgaagccttcatttcaattttctacatgacagcactaacgtgaatgtgtaaacgaaggttgtgtttgctcgactgacgctattgtactagttcacttgttgttcctgaaataacctttggagtgttcgcag

Basic information

species Physcomitrella patens
transcript PP1S132_95V6.1
intron # 8
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|208348540|gb|DC905819.1|DC905819
EST:     AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAG                         GGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT
genomic: AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT
EST: gi|67726923|gb|BJ977182.1|BJ977182
EST:     AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAG                         GGATTCGCTAGTGGAAGTCTGGACCAAGACGCCCATGCTGTTCGCTTATTT
genomic: AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT
EST: gi|67718471|gb|BJ968730.1|BJ968730
EST:     AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAG                         GGATTCGCTAGTGG
genomic: AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGG
EST: gi|100356048|gb|BY946170.1|BY946170
EST:     AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAG                         GGATTCGCTAGTGGAAGTCTGGACAAAGA
genomic: AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGGAAGTCTGGACAAAGA
EST: gi|100446010|gb|CJ970309.1|CJ970309
EST:     AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTNGACTGTGCATACCAG                         GGATTCNCTAGTGGA
genomic: AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGGA
EST: gi|162196336|gb|FC375406.1|FC375406
EST:     AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAG                         GGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT
genomic: AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT
EST: gi|162267156|gb|FC443387.1|FC443387
EST:     AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAG                         GGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT
genomic: AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT
EST: gi|162263809|gb|FC438428.1|FC438428
EST:     AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAA                         GGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT
genomic: AGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTT

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), 33 (downstream exon)
Score: 11

CAATCCCACTGGTGTTGACCCGACTGAAGAGCAGTGGGAAGGGATTCGACAGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgtt ... gtgttcgcagGGATTCGCTAGTGGAAGTCTGGACAAAGACGCCCATGCTGTTCGCTTATTTGTAGCTGATGGTGGGGAATGTTTTGTTGCACAAAGTTATGCTAAGAACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCCCACTGGTGTTGACCCGACTGAAGAGCAGTGGGAAGGGATTCGACAGGTTATTAGAAGCAAGCATCAGCTTCCCTTTTTTGACTGTGCATACCAGgtattttgttactattggattcaattttggtcatttctcactttatttttttattattttgaagccttcatttcaattttctacatgacagcactaacgtgaatgtgtaaacgaaggttgtgtttgctcgactgacgctattgtactagttcacttgttgttcctgaaataacctttggagtgttcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT