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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaaactctggagcaattaataatataagcgtttcggtgcctacgaagatgtttttcgcacccctatgtgttagtttaaatttttcacatgttttaccatgattgtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAA

Basic information

species Physcomitrella patens
transcript PP1S11_173V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S11_173V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
gtaattaaactctggagcaattaataatataagcgtttcggtgcctacgaagatgtttttcgcacccctatgtgttagtttaaatttttcacatgttt--taccatgattgtacttgc--agCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAA
                  ||  | |  || ||     | || |  |  | || |  ||   ||| |  |   || |   |  |  || |||     ||  ||   ||||    ||||   ||  |||||||||||||||||||| ||||||||||||||||| | || ||||||||  | ||||||  | | | | ||||  |  |||||    ||||||| 
-----------------aaaacattgctacaa-----taggagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG

upper sequence: PP1S11_173V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G094051_T03 (Zea mays), 3'ss of exon 5
gtaattaaactctggagcaattaataatataagcgtttcggtgcctacgaagatgtttttcgcacccctatgtgttagtttaaatttttcacatg-ttttaccatgattgta---cttgc--agCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAA
                      || || ||||      | ||||||       |  ||   ||| |      || |   | |  |  |||  |||   |||| |   | | |   ||||   ||  |||| ||||||||||||||| ||||||||||||||||| | || || |||||  | ||||||  | | | | ||||  |  |||||    ||||||| 
---------------------aaaaaacataaagcagacagtgcctg---gagtagttcctgcatcttagcttggtgactcatctgcttctgatgaccttactaaagtggcaaatcttgtttagGTACCCAAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAAGCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG

upper sequence: PP1S11_173V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
gtaattaaactctggagcaattaataatataagcgtttcg-gtgcctacgaagatgtttttcgcacccctatgtgttagtttaaatttttcacatg-ttttaccatgattgta---cttgc--agCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAA
                          | | |||| |   |  | |   |     |  ||   ||| |      || |   | |  |  |||  |||   |||| |   | | |   ||||   ||  |||| |||||||| |||||| ||||||||||||||||| | || || |||||| | ||||||  | | | | ||||  |  |||||    ||||||| 
-------------------------gaaaaaagcataaagcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG

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|7147844|gb|AW509766.1|AW509766
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|208365775|gb|DC951038.1|DC951038
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162206553|gb|FC382922.1|FC382922
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|18363812|gb|BJ195884.1|BJ195884
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGA
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGA
EST: gi|37821482|gb|BJ579548.1|BJ579548
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|67694029|gb|BJ954262.1|BJ954262
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162227524|gb|FC403466.1|FC403466
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162209025|gb|FC385577.1|FC385577
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162275286|gb|FC451262.1|FC451262
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|37834457|gb|BJ592469.1|BJ592469
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162230791|gb|FC406422.1|FC406422
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|37840975|gb|BJ598983.1|BJ598983
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162209026|gb|FC385578.1|FC385578
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|67700234|gb|BJ960467.1|BJ960467
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162230790|gb|FC406421.1|FC406421
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162227523|gb|FC403465.1|FC403465
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATTTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162259014|gb|FC435125.1|FC435125
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|162259015|gb|FC435126.1|FC435126
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
EST: gi|208391789|gb|DC937979.1|DC937979
EST:     GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG                         CAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG
genomic: GAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGG

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: 41

ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGGgtaattaaac ... gtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccctatgtgttagtttaaatttttcacatgttttaccatgattgtacttgcagCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAA
               tttaaatttttcacat  TA-rich tract