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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtaaatggcgatggtgggtgctcggatcacgtggagagggcgaggggctgtatgttctgagcttgtgcagaatagatgtgttactaggaggatcgtgtgtgggggtgggttatggcggtagtgcggggagatttctggccagggcttacactcaaatagaatacgtgtggtgtgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCTGCCTCCGATTCCCTGGGCAGCTAAACTCCGATCTGCGAAAGTTGGCTGT

Basic information

species Physcomitrella patens
transcript PP1S93_158V6.1
intron # 2
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|100445531|gb|CJ975680.1|CJ975680
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
EST: gi|162154149|gb|FC330592.1|FC330592
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
EST: gi|162161971|gb|FC338554.1|FC338554
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
EST: gi|100391126|gb|BY953136.1|BY953136
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCCTCGT                         TTGGCGACTTGGAAC-ATCTGATTTCGGCGA
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTG-AACCATCTGATTTCGGCGA
EST: gi|162225192|gb|FC402232.1|FC402232
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
EST: gi|162162609|gb|FC338911.1|FC338911
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
EST: gi|162209457|gb|FC386090.1|FC386090
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACNATGAGCGG
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGG
EST: gi|100418154|gb|BY993360.1|BY993360
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATC
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATC
EST: gi|162275313|gb|FC451497.1|FC451497
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
EST: gi|162156965|gb|FC333119.1|FC333119
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
EST: gi|100361062|gb|BY946895.1|BY946895
EST:     AACGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACTTGAACCATCTG
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTG
EST: gi|208379149|gb|DC927292.1|DC927292
EST:     AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGT                         TTGGCGACNTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
genomic: AGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCT
EST: gi|100415800|gb|BY993009.1|BY993009
EST:     GCGCTATATGACATCTGCTTCCGGACACTGAAACTCAATACTTCCT-CGT                         TTGGCGACTTGAA
genomic: GCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACT-CCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAA

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: 28

GTGCACCAGTTGGTAGAGAATGCCGACGAGTGCATGGTGTTGGACAACGAAGCGCTATATGACATCTGCTTCCGGACACTGAAACTCATTACTCCTTCGTgtaagtgtaa ... tgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCTGCCTCCGATTCCCTGGGCAGCTAAACTCCGATCTGCGAAAGTTGGCTGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatttctggccagggcttacactcaaatagaatacgtgtggtgtgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCTGCCTCCGATTCCCTGGGCAGCTAAACTCCGATCTGCGAAAGTTGGCTGT
               ggcttac  putative branch site (score: 28)
                          aaatagaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtaaatggcgatggtgggtgctcggatcacgtggagagggcgaggggctgtatgttctgagcttgtgcagaatagatgtgttactaggaggatcgtgtgtgggggtgggttatggcggtagtgcggggagatttctggccagggcttacactcaaatagaatacgtgtggtgtgtggtgcagTTGGCGACTTGAACCATCTGATTTCGGCGACAATGAGCGGTATCACTTGCTGCCTCCGATTCCCTGGGCAGCTAAACTCCGATCTGCGAAAGTTGGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT