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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactttcggtctatactctgagtgatcccttgcttaaatctattcggcatttgatgtggctcatatatgttgataaatcatcttggtgctcgtatgagaaactgttgagagctgctaggacctacctgtgtggtgtgctgtatgatacagcttctgagtctatttgttgtacccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTGTATGCTGCATTCGAAGGAATTCTAAGTCGCCATCTTCCTTCATAGGTCT

Basic information

species Physcomitrella patens
transcript PP1S460_21V6.1
intron # 8
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|37847045|gb|BJ605053.1|BJ605053
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162218293|gb|FC394467.1|FC394467
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162210751|gb|FC386647.1|FC386647
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162200373|gb|FC376372.1|FC376372
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCC
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCC
EST: gi|162200372|gb|FC376371.1|FC376371
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|208378297|gb|DC922996.1|DC922996
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAAGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162210750|gb|FC386646.1|FC386646
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162153016|gb|FC330046.1|FC330046
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162218292|gb|FC394466.1|FC394466
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|37823510|gb|BJ581576.1|BJ581576
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162280233|gb|FC456250.1|FC456250
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162186579|gb|FC363343.1|FC363343
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|18340796|gb|BJ172827.1|BJ172827
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162183765|gb|FC360682.1|FC360682
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|67696472|gb|BJ956705.1|BJ956705
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162183764|gb|FC360681.1|FC360681
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162181413|gb|FC357117.1|FC357117
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|162172964|gb|FC347874.1|FC347874
EST:     CATTTTTAGCANACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|18334775|gb|BJ166792.1|BJ166792
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
EST: gi|37836769|gb|BJ594777.1|BJ594777
EST:     CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAG                         GAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG
genomic: CATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTG

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-Seq library.


Block sizes: 28 (upstream exon), 32 (downstream exon)
Score: 8

GGCTCGGTTGTCATACGAGCAATTCAGCTCATTTTTAGCAAACATTAAGGAGCTTAATGCACATCGTCAAACACGGGAGgtaaaacttt ... cccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTGTATGCTGCATTCGAAGGAATTCTAAGTCGCCATCTTCCTTCATAGGTCT































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtggtgtgctgtatgatacagcttctgagtctatttgttgtacccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTGTATGCTGCATTCGAAGGAATTCTAAGTCGCCATCTTCCTTCATAGGTCT
                                  tatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaactttcggtctatactctgagtgatcccttgcttaaatctattcggcatttgatgtggctcatatatgttgataaatcatcttggtgctcgtatgagaaactgttgagagctgctaggacctacctgtgtggtgtgctgtatgatacagcttctgagtctatttgttgtacccattgcagGAGACTCTGGCGAATGCTGAGGATATCTTTGGCCCAGAGAACAGGGACCTGTATGCTGCATTCGAAGGAATTCTAAGTCGCCATCTTCCTTCATAGGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA