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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaggctgtcgatatgattttagagctggctgtgctaggtcatctttccattgtctgcctattattattaacttgtgttcattcttttccgtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATGGGGCTATTTGAGAAGCGGCGTGCTAGGAAGTTTTTCATCTTTGTCCAGA

Basic information

species Physcomitrella patens
transcript PP1S20_16V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S20_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G30050.1 (Glycine max), 3'ss of exon 4
-------------------------------------------gaaggctgtcgatatgatttt--agagctggctgtgctaggtcatctttc-cattgtctgcctattattattaacttgtgttcattcttttccgt---ttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATGGGGCTATTTGAGAAGCGGCGTGCTAGGAAGTTTTTCATCTTTGTCCAGA
                                            |  |||     | | || ||  | |  |   | |   |   | |||| |  |||| |       |  |   |   | | || |||  | |   |   ||   ||| | |||||||||||| | |  || || |||||| ||||||| || || ||||| || ||||||||||| |||||| ||||||| ||||||| ||||||  
gtaggcagcatattcatcatgttctttattttcttttgtacacaactgctactttttttatattgcaaacttaaatttcacaaaacctcttgcatattgacaaaaatcttatgacagaatatctttatttatatatatattttttttagATTTACAAAGTTCCAGCAACAGATGTTGAAGCACTGAAGTCACCATTAATGGGTCTGTTTGAGAAGCGCCGTGCTCGGAAGTTCTTCATCTATGTCCAAG
















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|162166683|gb|FC342652.1|FC342652
EST:     AGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: AGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|100422189|gb|BY957901.1|BY957901
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|162196487|gb|FC375440.1|FC375440
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|100423739|gb|BY976524.1|BY976524
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|162180984|gb|FC358638.1|FC358638
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|100352808|gb|BY945459.1|BY945459
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|162187203|gb|FC363153.1|FC363153
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|162229881|gb|FC404334.1|FC404334
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|208387306|gb|DC933057.1|DC933057
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAANTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
EST: gi|162257732|gb|FC433659.1|FC433659
EST:     ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAG                         GTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG
genomic: ACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATG

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), 31 (downstream exon)
Score: 13

GGCAAATGGCACCCTTGTGAGAGTTCTCATCCACACGGATGTCACAAAATACCTACTGTTTAAGGCTGTGGACGGCAGCTACGTCTATAAGCAGGGAAAGgtgcgtcgtt ... gtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATGGGGCTATTTGAGAAGCGGCGTGCTAGGAAGTTTTTCATCTTTGTCCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccattgtctgcctattattattaacttgtgttcattcttttccgtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATGGGGCTATTTGAGAAGCGGCGTGCTAGGAAGTTTTTCATCTTTGTCCAGA
                    tattaac  putative branch site (score: 13)
                              tgttcattcttttccg  putative PPT
              tattattattaacttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaggctgtcgatatgattttagagctggctgtgctaggtcatctttccattgtctgcctattattattaacttgtgttcattcttttccgtttccatagGTGTACAAAGTTCCATCTAATGACGTGGAAGCATTGAAGTCTCCTTTGATGGGGCTATTTGAGAAGCGGCGTGCTAGGAAGTTTTTCATCTTTGTCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC