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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA

Basic information

species Physcomitrella patens
transcript PP1S450_22V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctg-aaaactgcgtc-ttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
                                       | |  || |  |||| | ||| |     |    ||  |   ||||||  || |    ||     || ||||  ||  | |    || |    | |||||   || |  |||  ||  | |  |||||||||||||||||| || ||||||||| | || |||||||| |||||||| || ||||| || ||
---------------------------------------gtatggttt--tctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcagctgtttgaagattgccattttgtgcaagtgatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
                                                                                       |  | |  | || ||||    |       |||   |||       |  ||||    |  |  |  ||      ||||||||| | |||||||| ||||||||| | |||||||||||||||||||| || ||||| || ||
--------------------------------------------------------------------------------------gtacgtttgtttctctgcacatttgcttcatcacctgttctgtcctgtgtaaa---catgggcttctgc-----agGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 2
----------------------------gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgcttt-ctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtatt--agGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
                               || |    |  ||      |||   |     |   | |   |||| ||  ||  |   |||| | |  | | |  |||        ||||   || | ||  |  ||| |   ||   |||| |       |      |||  |  |  || | |  |  ||||||||||||||||| || ||||||||| | ||||||||||||||||| || || ||||| || ||
gtacgtcacgtgactctgttcttattacacgcaaaaaacaacctatgattgtgtcgtgtgctcctgttctgtgtctcttacgttccctaagcttaaacttttaaccacttaac----agatagacttcatgtgtggctgtgatcgttccgagtgttgaaattacggttttgtccttttccttttctgatgcagGTACTTCTTGAACGTGATTTTCAACATCCTTAACAAGAAGATCTACAATTACTTCCCCTATCCATA

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G32190.1 (Glycine max), 3'ss of exon 2
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtc--tcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
                                             | | || ||||  | || | |  | |    | |    | ||| | |   ||||| ||| |  |  |||      ||    |||       |||    | | ||||            ||||||||||||||||| || ||||||||| | ||||||||||||||||| || || ||||| || ||
---------------------------------------------tgtgttgtgtccatgaagaacagaaagacttta---ttacgtgtggctgtgatcgccccgagtgttgaaattacca----ttttgtccttattcttttctgatgc------------agGTACTTCTTGAACGTGATTTTCAACATCCTCAACAAGAAGATCTACAATTACTTCCCCTATCCATA

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgt-cttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaa-aatgtaatgcttgttgtgtatt---agGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
                                     | | | | |  |  |  | |       ||| | ||    |  |||||  ||| ||  |||     || |||    | ||       ||||   |   ||| |   | | || ||  ||  |||||   |||||||||||||| || || ||||||||| | |||||||||||||| || || || || || |||||
-----------------------------------gtacgtatcattcacgcgcttttc----ttaaaacgtt---atcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 2
gtacacattctactcttgtgcagtgctattg--agccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
               | |  ||   |  ||   | | ||   || |  | ||||| | ||||| |  |  | |  | ||||     |  |||    |  |||||| ||||||         || || |       |  ||| |||| |  ||          ||||| ||| | ||||| || ||||||||| | |||||||||||||||||||| || || || || ||
--------------gtaggtcatcaccgttaccaactaacaacatctacaattctct-tcaacggtcagaaagagtcaaaataaaatggtgattcaaaatccctg-tttctg---------ggtgtcttt-----accaaattgtacttttt---------cagGTATTTCCTCAACGTTATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCATATCCTTA

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 2
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgctttc--tgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
                                                                                      | |  ||| | |  || | |||  |       |       ||        |  |||||  ||  |  || |     ||||| ||  | || || |||||||||||| | ||||||||||||||||| |||||||| || || ||
-------------------------------------------------------------------------------------gtaggcatgctttttcttccttccttattttgcttttccacttttctctcttgcaaatgagatcttccttcttg--cagGTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATA

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 1
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
                                                                                 |          |  ||| ||| | || |  |    ||    |||       |   |  |  |  | ||| |||      ||||| ||  | || || |||||||||||| | ||||||||||||||||| |||||||| || || ||
---------------------------------------------------------------------------------gtaggcatgctttttcttccttccttttttgcttttccactgttctctcttgcaaatgagatcttccttcttgc-----agGTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATA

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|100367304|gb|BY984874.1|BY984874
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTTCA-CATCATGAACAAGAAGATCTACAACT
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTT-CAACATCATGAACAAGAAGATCTACAACT
EST: gi|67709586|gb|BJ965402.1|BJ965402
EST:     TTTCTCGCCATGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|100397819|gb|BY990417.1|BY990417
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|100384601|gb|BY950591.1|BY950591
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|67719082|gb|BJ969341.1|BJ969341
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|100449284|gb|CJ973583.1|CJ973583
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|67716735|gb|BJ966995.1|BJ966995
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|208378082|gb|DC932448.1|DC932448
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAANAANATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|67704465|gb|BJ964698.1|BJ964698
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACNACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|100436251|gb|BY979454.1|BY979454
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|67716900|gb|BJ967159.1|BJ967159
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|67717698|gb|BJ967957.1|BJ967957
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|100443152|gb|BY981778.1|BY981778
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAAC
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAAC
EST: gi|208392058|gb|DC941906.1|DC941906
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|208360889|gb|DC934785.1|DC934785
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|208369404|gb|DC936093.1|DC936093
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|67717101|gb|BJ967360.1|BJ967360
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|67717918|gb|BJ968177.1|BJ968177
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|18361942|gb|BJ194009.1|BJ194009
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
EST: gi|18347795|gb|BJ179842.1|BJ179842
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAA
EST: gi|67578440|gb|BJ950607.1|BJ950607
EST:     TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTG                         GTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA
genomic: TTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTA

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: 80

GGTTGCGATGGAGAGAACGGAAGAGGCTCAAGGCTTTCTCGCCAAGAATCCCGCTTTGGTCACTGGATTTTTCTTCTTCGCCTGgtacacattc ... tgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
                        agattaaaatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgtcttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG