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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC

Basic information

species Physcomitrella patens
transcript PP1S156_120V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
 | |  | |   |||||   ||   || |   ||  |  ||||  | |  | | |  || |   ||  | ||    |||||||||         |  ||||| |||||||| ||||| || || ||||| |||||||||||| | || |||||| || |||| ||||| |||||||||||||||||  |||| |||||||
gtgagcttacgactgctcttatctagccaatctaaat--agtt--ctattagttggattcctgttgatgtttgctatttcttttgcccca----tttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC

upper sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
-ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
 | | || |       ||    || ||| ||  |   |||     ||    ||| | | |  |||  ||  || |||||   |||    || | | | |||||||| || || |||||||| || ||||| |||||||||||   ||| |||||| |  ||||||| || ||||| |||||||||||| |||| |||||||
gtgagctgcttaatcact---gttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactac-cagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC

upper sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
-ttaacttcaattctgcttgaattgtgcaataatagtttgagttatcca-gcaatagatttt--cacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
 ||    |    |||     | |    ||||  || |||   |||| ||  ||  ||  |||   |    |   || ||    | |||| |||||||  | |||||  | ||||| || || ||||| ||||| |||||||| || || || |||||  || | |||||||||||||| ||||||||||||||||| || ||| 
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaa--cacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

upper sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttt--------tgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
              | |||   | | ||  ||   ||  |  | ||  |   || ||| |  ||| ||  |     ||  ||         ||  ||| || | ||||||  | |||||||| || || || ||||| |||||||| || || || || ||  || | |||||||| ||||||||||| ||||||||||| |||||||
--------------gtttgtgctcttcagaaa--attaaatctctcttgtgtta-attgtttcctatgtttccaaattcattgatagaatgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC

upper sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------ttaacttcaattctgcttgaattgt-gcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
                                 |||  ||  ||  ||     |||||  |     || | | || | ||   | ||   ||   | || | |       |||  | || |||  | |   |||||||| ||||| ||||| ||||| ||||| |||||||||||  | || |||||  || | || ||||| ||||| ||||| |||||||||||||| || |
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctatt--ttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 3'ss of exon 2
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatc-cagcaatagattttcacc-tgtg-gcttatgctt-tcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
   |  |  || | ||          ||  |   |  |       | || |   |  || ||||| || | || |  || | ||  || | |    |   | ||||||| || ||||||     ||||||||| ||||||||||| ||||| |||||| | |||||||| || |||                            
--catgtgcatgcagc--agcccaaccagcacgcgcctagacccccacaccgcaaccttctcaccctgcgcgcctgcgcctgtcccttttgtcaccacatgtagATTCTGTTCGTGATCCAGTCGCCCGATGTCTTCAAGAGCCCCGCCTCGGACACCTACATCATCTTCGGCGAG----------------------------

upper sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
                                 || ||| |||          |||        |   |  ||   |  ||| || ||     ||  ||||| || ||||||||||| |||||||| || ||||||||||| || || ||||| || ||||||||||| ||||||||||||||||| |||||||| ||||
------------------------------gtaagcttgcgttggtagatcgaaga-----gaatagagactaacttcgcttctggttc----tttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

upper sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ21445 (Selaginella moellendorffii), 3'ss of exon 1
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
                                     | || |  |  | | |||||         | |  | |   |||  |    |||   ||  ||||| || || |||||||| |||||||| || ||||||||||| || || ||||| || ||||||||||| ||||||||||||||||| |||||||| ||||
------------------------------------gtaagcttgc--gtagtagatgaaagagaatagagtctaacttcgctc--cttgttctttccagATACTGTTCGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

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|162226117|gb|FC401577.1|FC401577
EST:     TGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAAT                         ATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGAC
genomic: TGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAATgtatattctg ... gaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGAC
EST: gi|67721295|gb|BJ971554.1|BJ971554
EST:     TGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAAT                         ATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGAC
genomic: TGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAATgtatattctg ... gaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGAC
EST: gi|162264800|gb|FC440367.1|FC440367
EST:     TGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAAT                         ATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGAC
genomic: TGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAATgtatattctg ... gaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGAC
EST: gi|162225495|gb|FC401234.1|FC401234
EST:     TGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAAT                         ATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGAC
genomic: TGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAATgtatattctg ... gaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGAC

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: 34 (upstream exon), 34 (downstream exon)
Score: 22

GCAGAGTCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTGGGTATGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAATgtatattctg ... gaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC
     aatagatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT