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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgtctaagcccccatgacctgagtcaggcgcacatgtctcagaggttctaataccgctagcccacaccgtgtcacgttaatgttaaaatctaagttgaattggaatgattgccctgacttggcagatgcgcactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTCACCCTTTGAAGGTCTCCTTGGAAGAACTTTACAATGGCACATCAAAGAA

Basic information

species Physcomitrella patens
transcript PP1S342_16V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S342_16V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 3
gtatgcgtctaagcccccatgacctgagtcaggcgcacatgtctcagaggt--tctaataccgctagcccacacc-gtgtcacgttaatgttaaaatctaagttgaattggaatgattgccctgacttggcagatgcgcactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTCACCCTTTGAAGGTCTCCTTGGAAGAACTTTACAATGGCACATCAAAGAA
                   | |   ||  |   |  | || |||      |  | || |    | |      ||   | ||  ||  |  || |||   |  || ||||   ||   |   |||| |    ||   |  | |||| ||||||  || ||    |  |  |  | |||| | |||||||||||||||| ||  |||||||||| || ||||| ||  | || |||||||||||||||||
------------------gtaagaggatgcttacttaaatttcttgatctttatttattttttcaaatgtgtacttatttcctgtctacctttaaagaaattttcaatt---atatatttactgattcccaagtatctaattttgtagGTGGTGGTAGCTCAAGAGGAAGAAGGCAGAAACGAGGTGAAGATGTTGTGCATACTTTGAAGGTTTCTTTGGAGGACTTGTATAATGGCACATCAAAGAA
















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|208359881|gb|DC939269.1|DC939269
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|100401219|gb|BY990892.1|BY990892
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|100414304|gb|BY992711.1|BY992711
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|162174909|gb|FC351701.1|FC351701
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|162189947|gb|FC365611.1|FC365611
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|208380035|gb|DC914585.1|DC914585
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|162242594|gb|FC414985.1|FC414985
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|100359037|gb|BY946814.1|BY946814
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|162195909|gb|FC375642.1|FC375642
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|100357768|gb|BY946564.1|BY946564
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|208369628|gb|DC936362.1|DC936362
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|67507785|gb|BJ940663.1|BJ940663
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGA
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGA
EST: gi|162152418|gb|FC327981.1|FC327981
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|22492240|gb|BU052163.1|BU052163
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|100409753|gb|BY956088.1|BY956088
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|100415464|gb|BY992856.1|BY992856
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|162180208|gb|FC355525.1|FC355525
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|162157608|gb|FC332930.1|FC332930
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|162185740|gb|FC362088.1|FC362088
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|208366024|gb|DC935841.1|DC935841
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|100448738|gb|CJ973037.1|CJ973037
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
EST: gi|162162054|gb|FC338845.1|FC338845
EST:     ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAG                         GTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC
genomic: ATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTC

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: 88

GAGGATGCCCTGAAGGAGGGGATGGGCGGAGGCGGTGGCGGACACAATCCATTTGATATCTTTGAGTCGTTCTTTGGCGGAGGCGGTAGTCCATTTGGAGgtatgcgtct ... cactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTCACCCTTTGAAGGTCTCCTTGGAAGAACTTTACAATGGCACATCAAAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatctaagttgaattggaatgattgccctgacttggcagatgcgcactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTCACCCTTTGAAGGTCTCCTTGGAAGAACTTTACAATGGCACATCAAAGAA
                          ccctgac  putative branch site (score: 88)
         ttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgtctaagcccccatgacctgagtcaggcgcacatgtctcagaggttctaataccgctagcccacaccgtgtcacgttaatgttaaaatctaagttgaattggaatgattgccctgacttggcagatgcgcactttgcagGTGGCAGTGGCAGGGGCAGCCGGCGACAGAGAAGAGGTGAAGATGTTGTTCACCCTTTGAAGGTCTCCTTGGAAGAACTTTACAATGGCACATCAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA