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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactgtgaacctatcataaaaaatggatgtatagcgaggcaactaattgtcaaaactgcattcacctggcagtgcctaaaggacattcagaaaagttatcaggatttgttttccttcacaagcattcgatcaagatggatattattttttccgctctttcttatctattaactttgaatcatttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACGTTGCAAGCCCTTTAAATATACGTACGAGAAGGAGATTGTAATGTACGCA

Basic information

species Physcomitrella patens
transcript PP1S54_267V6.1
intron # 5
splice site 3'
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|100385871|gb|BY951065.1|BY951065
EST:     TGTTGCTGAGACCATCTTGGCTCA-CATTTGT-CGTGGTGACATTGCTAG                         ATTAGCGAGATGTACTTCGATTAT
genomic: TGTTGCTGAGACCATCTTG-CTCAACATT-GTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTAT
EST: gi|162160655|gb|FC337204.1|FC337204
EST:     GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAG                         ATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG
genomic: GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG
EST: gi|208386768|gb|DC937160.1|DC937160
EST:     GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAG                         ATTAGCGAGATGTACTTCGATTATANCTGGAG
genomic: GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAG
EST: gi|100379791|gb|BY949946.1|BY949946
EST:     TGTTGCTGAGACCATCTTGGCTCA-CATTTGT-CGTGGTGACATTGCTAG                         ATTAGCGAGATGTACTTCGATTATNACTGGAGAAGAAGGTGCTTTGCCCCA
genomic: TGTTGCTGAGACCATCTTG-CTCAACATT-GTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCC--A
EST: gi|162160669|gb|FC337205.1|FC337205
EST:     GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAG                         ATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAANGTGCTTTGCCACG
genomic: GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG
EST: gi|208354247|gb|DC957439.1|DC957439
EST:     GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAG                         ATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG
genomic: GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG
EST: gi|208358391|gb|DC943222.1|DC943222
EST:     GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAG                         ATAAGCGAGATGTACTTCGATTATAACTGGA
genomic: GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGA
EST: gi|37821355|gb|BJ579421.1|BJ579421
EST:     GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAG                         ATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG
genomic: GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG
EST: gi|208372809|gb|DC956210.1|DC956210
EST:     GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAG                         ATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG
genomic: GATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACG

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: 19 (upstream exon), 23 (downstream exon)
Score: 2

GGGCTGCTAAGATGAAAGCTGTCAAGATGGCTACTGGTCACAATGCTGATGATGTTGCTGAGACCATCTTGCTCAACATTGTTCGTGGTGACATTGCTAGgtaagactgt ... ttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACGTTGCAAGCCCTTTAAATATACGTACGAGAAGGAGATTGTAATGTACGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattattttttccgctctttcttatctattaactttgaatcatttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACGTTGCAAGCCCTTTAAATATACGTACGAGAAGGAGATTGTAATGTACGCA
                            tattaac  putative branch site (score: 2)
                   tttcttatctattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactgtgaacctatcataaaaaatggatgtatagcgaggcaactaattgtcaaaactgcattcacctggcagtgcctaaaggacattcagaaaagttatcaggatttgttttccttcacaagcattcgatcaagatggatattattttttccgctctttcttatctattaactttgaatcatttgcatgcagATTAGCGAGATGTACTTCGATTATAACTGGAGAAGAAGGTGCTTTGCCACGTTGCAAGCCCTTTAAATATACGTACGAGAAGGAGATTGTAATGTACGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT