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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggagtttttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG

Basic information

species Physcomitrella patens
transcript PP1S56_243V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S56_243V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 1
tgggagtttttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG
 | |||| || | | | ||  ||  |  |       || ||  | | |  |   |      ||||||     |   |   |   | ||          |||| || |||||||||||||| ||||| || ||||| ||  ||  | | |||  ||| |||   |||||||||||||| |||||||| |||||||| ||||
-gtgagtcttctcctgctccgtccatccgactgcggtgattagaatttgatccat---gggtttgat----ttagcccctgc--tttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG

upper sequence: PP1S56_243V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G022619_T02 (Zea mays), 3'ss of exon 1
---------------tgggagtttttttcgggtctttctgttt--gttcatcatggtttcagtgtactt--tttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG
                 |  |  |  | |   ||||  ||| |   | |  |  |  ||   | | |    | | |   || |      |||  ||       |||  || | |   |||| || |||||||||||||| || || || ||||| ||  | ||| |||||  ||| |||   |||||||||||||| |||||||||||||| || ||||
gtaagcctaccgccgccgccgcctcctccatctcttcttgtcttgatccgacgcgtcttttctctccccggtgtttctgatctc-caccgcttttctgttatatgttctggtgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCGACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACTAACGAGGTTCGCG

upper sequence: PP1S56_243V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
tgggagtttttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatc--aaggtcgtgtcttgttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG
       ||||   |  | ||   |       | ||  |    || ||  ||| | | |    |||   |  ||||    |  | |  || | |      |||||||||||||||||||||||||| ||||||| ||  | |   |  |||||   |||| |   ||| | |||||||| ||||| || ||||| || || |
-tttttcttttcctgaattttctcggcaaccaaacaaaggaatag-gtgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG

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|67718152|gb|BJ968411.1|BJ968411
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|162270822|gb|FC446851.1|FC446851
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|67704104|gb|BJ964337.1|BJ964337
EST:     TACCCTGCTTCGCACCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|37846767|gb|BJ604775.1|BJ604775
EST:     TCTCGGGGATTCCTGTACACCGCCATGAGCCTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCCAATGA
genomic: TCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCA-CCAATGA
EST: gi|18325024|gb|BJ157020.1|BJ157020
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|18360441|gb|BJ192503.1|BJ192503
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|162260389|gb|FC436068.1|FC436068
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G                         --------GTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|162206290|gb|FC382568.1|FC382568
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|67702617|gb|BJ962850.1|BJ962850
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|162235022|gb|FC411809.1|FC411809
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|18366391|gb|BJ198470.1|BJ198470
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|162264738|gb|FC440305.1|FC440305
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|67726640|gb|BJ976899.1|BJ976899
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|18372508|gb|BJ204110.1|BJ204110
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|7067002|gb|AW496857.1|AW496857
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|37852027|gb|BJ610035.1|BJ610035
EST:     TCTCGGGGATTCCTGTACACCGCCATGAGC-TTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|19780393|gb|BQ039555.1|BQ039555
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|208391446|gb|DC937594.1|DC937594
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|208394496|gb|DC953535.1|DC953535
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|37825253|gb|BJ583319.1|BJ583319
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|67703922|gb|BJ964155.1|BJ964155
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|208375525|gb|DC940523.1|DC940523
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|67727824|gb|BJ978083.1|BJ978083
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|7067340|gb|AW497195.1|AW497195
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|208398326|gb|DC912311.1|DC912311
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|67719554|gb|BJ969813.1|BJ969813
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|18346144|gb|BJ178187.1|BJ178187
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|18367074|gb|BJ199154.1|BJ199154
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|208353060|gb|DC926083.1|DC926083
EST:     CATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: CATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
EST: gi|19790807|gb|BQ042066.1|BQ042066
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAG

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), 30 (downstream exon)
Score: 18

CAGTGTGCGTCGGGGGTGTGGTTGGGAGGAAGGGCAGGCTGTCGCCCCGTTACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactttttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG
                        tgctgat  putative branch site (score: 18)
                                         tcttgttcc  putative PPT
     tttttctgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggagtttttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC