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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaacgtatcattctagtttgatctttctggaaccttgtgcgccattctgattttaccctcattacttacatcgtagtcatatatgtgggaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGCACAAACATATCAGCGACTTTACCAG

Basic information

species Physcomitrella patens
transcript PP1S2_595V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_595V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 5
aagaacgtatcattctagtttgatctttctggaaccttgtgcgccattctgattttaccctc---attacttacatcgtagtcatatatgtgg-----gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGCACAAACATATCAGCGACTTTACCAG
       | ||  | ||||||    |   | |||  | ||   | || || |  ||  | |    ||  ||||  |  | | | || || | |     |  ||||||| || ||||||||||||| ||| ||||||||||| |||||| |||| |||||  |    ||||| ||  | ||  | 
-------tttctgtttagtttttggtaaatagaaa-tagttatctatccttaacttgtcttgcaaatatcttatttacttgacctaaatatagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA

upper sequence: PP1S2_595V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 5
aagaacgtatcattctagtttgatctttctggaaccttgtgcgccattctgattttaccctcattacttacatcgtagtcatatatgtgg-----gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGCACAAACATATCAGCGACTTTACCAG
       | | |  ||  |||| |   |    |   || ||   | ||    | |    |  ||  ||||  |  ||| | || || | |     |  ||||||| || ||||||||||||| ||| ||||||||||| |||||| |||| |||||  |    ||||| ||  | ||  | 
---tttctgttaagct--tttggtaaatagaaataattatgtatccttaacttgtcttgcaaatatcttatttactagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA

upper sequence: PP1S2_595V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 5
aagaacgtatcattctagtttgatctttctggaaccttgtgcgccat---tctgattttaccctcattacttacatcgtagtcatatatgtgggaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGCACAAACATATCAGCGACTTTACCAG
 ||      ||   ||  ||| || | | |  ||  || ||    ||     | ||| |     | | ||||   | | |    |     | |  |  ||||| || ||||||||||||| ||| ||||||||||| |||||| |||| |||||  |    ||||| ||  | ||  | 
-aggcttagtctaccttttttaatttctgttaaagtttttggcaaatggaaataattatttgtccttaacttgtcttgcaaatttggtctttgttg--ttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCCGAGCAGTATCATCGGTTATATAAA

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|162157426|gb|FC333502.1|FC333502
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162267261|gb|FC442673.1|FC442673
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|18365122|gb|BJ197196.1|BJ197196
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162157425|gb|FC333501.1|FC333501
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|18327442|gb|BJ159445.1|BJ159445
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162182796|gb|FC359738.1|FC359738
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|37840995|gb|BJ599003.1|BJ599003
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162182797|gb|FC359739.1|FC359739
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|162267260|gb|FC442672.1|FC442672
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|37840717|gb|BJ598725.1|BJ598725
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|18335705|gb|BJ167726.1|BJ167726
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|208395624|gb|DC920242.1|DC920242
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|18363581|gb|BJ195653.1|BJ195653
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|208349216|gb|DC906358.1|DC906358
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
EST: gi|18363832|gb|BJ195904.1|BJ195904
EST:     ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAG                         CGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC
genomic: ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGC

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), 34 (downstream exon)
Score: 8

ATTAATAAAATTCAGTCATTGACCCCAAACATCGGAGTTGTCTACAGgttagtgctt ... gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGCACAAACATATCAGCGACTTTACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctgattttaccctcattacttacatcgtagtcatatatgtgggaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGCACAAACATATCAGCGACTTTACCAG
                   tacttac  putative branch site (score: 8)
                 attactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaacgtatcattctagtttgatctttctggaaccttgtgcgccattctgattttaccctcattacttacatcgtagtcatatatgtgggaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGCACAAACATATCAGCGACTTTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG