Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCAAAGAGTTCAACGCGAATAACATTAGGGATACATTTCGGTTGCTGCTGCAAATGAGCGTTGTGCTTATGTTCGGAGGGCAGCTGCCGGTTGTGAAGgtatgaattcatcttaagctcctcaataagttgcgagggctcgctgctaggctcgatgaagcgtcaagagcggacggctgtaatttgtcgagcattttgtaatgtaatataacgttgtcgtcctaagtaatttgcagctcgcgatttaagattgggttttgaggaatgtgagcag

Basic information

species Physcomitrella patens
transcript PP1S36_31V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S36_31V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM5G828182_T02 (Zea mays), 5'ss of exon 1
CTTCAAAGAGTTCAACGCGAATAACATTAGGGATACATTTCGGTTGCTGCTGCAAATGAGCGTTGTGCTTATGTTCGGAGGGCAGCTGCCGGTTGTGAAGgtatgaattcatct-taagctcctcaataagttgcgagggctcgctgctaggctcgatgaagcgtcaagagcggacggctgtaatttgtcgagcattttgtaatgtaatataacgttgtcgtcctaagtaatttgcagctcgcgatttaagattgggttttgaggaatgtgagcag
|||||| ||||||||||| || ||||| ||||| || || ||  | || |||||||||  ||||||||| ||||||||||| ||| |||| || || ||||||  | |  ||   |||  ||  |   ||| |   || | |    | | |  ||| | |  | ||| |  ||  |   |  |   |       ||  | | |                                                                         
CTTCAAGGAGTTCAACGCCAACAACATCAGGGACACCTTCCGCGTCCTCCTGCAAATGTCCGTTGTGCTCATGTTCGGAGGCCAGATGCCTGTCGTCAAGgtagtattgtataaataaaatcgcctcaaagcttt-agtgttgatcgatcgaatcgtttagacatcatgcccgctc--ttacagcctaaattaaatcctatta-------------------------------------------------------------------------
















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|100399449|gb|BY972724.1|BY972724
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|162167806|gb|FC344536.1|FC344536
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100444546|gb|BY964244.1|BY964244
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTTAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|67508054|gb|BJ940926.1|BJ940926
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100416467|gb|BY975403.1|BY975403
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100379507|gb|BY949803.1|BY949803
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100399119|gb|BY954209.1|BY954209
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|162194173|gb|FC369685.1|FC369685
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|67508242|gb|BJ941112.1|BJ941112
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|208357209|gb|DC934261.1|DC934261
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100389429|gb|BY988907.1|BY988907
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|67717150|gb|BJ967409.1|BJ967409
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|162248092|gb|FC420097.1|FC420097
EST:     TGCAAATGAGCGTTGTGCTTATGTTCGGAGGGCAGCTGCCGGTTGTGAAG                         GTTGGAAGAATGGCTGGACAATTTGCCAAACCCAGATCAGCCGATATGGAA
genomic: TGCAAATGAGCGTTGTGCTTATGTTCGGAGGGCAGCTGCCGGTTGTGAAGgtatgaattc ... atgtgagcagGTTGGAAGAATGGCTGGACAATTTGCCAAACCCAGATCAGCCGATATGGAA
EST: gi|162256237|gb|FC432293.1|FC432293
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100401453|gb|BY991010.1|BY991010
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|67704588|gb|BJ964821.1|BJ964821
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTTGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|67508221|gb|BJ941092.1|BJ941092
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100388855|gb|BY988731.1|BY988731
EST:     GCAGCAACCTTACGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: GCAGCAACCTT-CGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100444732|gb|BY982561.1|BY982561
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|162187914|gb|FC364488.1|FC364488
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|162270228|gb|FC447240.1|FC447240
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|162163356|gb|FC339682.1|FC339682
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100377952|gb|BY949605.1|BY949605
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100362696|gb|BY947482.1|BY947482
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100447277|gb|CJ971576.1|CJ971576
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|100376557|gb|BY986224.1|BY986224
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|162160220|gb|FC337117.1|FC337117
EST:     GTTGTGCTTATGTTCGGAGGGCAGCTGCCGGTTGTGAAG                         GTTGGAAGAATGGCTGGACAATTTGCCAAACCCAGATCAGCCGATATGGAA
genomic: GTTGTGCTTATGTTCGGAGGGCAGCTGCCGGTTGTGAAGgtatgaattc ... atgtgagcagGTTGGAAGAATGGCTGGACAATTTGCCAAACCCAGATCAGCCGATATGGAA
EST: gi|67571977|gb|BJ944801.1|BJ944801
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|67568922|gb|BJ941746.1|BJ941746
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
EST: gi|162151761|gb|FC328618.1|FC328618
EST:     TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT
genomic: TGCAGCAACCTTCGTACCCGGACCCTGAGAAGGTCGCTGAGGTTGTGAAGCAGATGGAAGGATACCCACCTCTCGTGTTCGCGGGTGAGTCGCGCAGTTTGGAGGAGCGCTTAGGGGAGGCCGCTT

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), 35 (downstream exon)
Score: 30

CTTCAAAGAGTTCAACGCGAATAACATTAGGGATACATTTCGGTTGCTGCTGCAAATGAGCGTTGTGCTTATGTTCGGAGGGCAGCTGCCGGTTGTGAAGgtatgaattc ... atgtgagcagGTTGGAAGAATGGCTGGACAATTTGCCAAACCCAGATCAGCCGATATGGAAGACGTGAATGGAGTATCGCTGCCGAGTTACCGGGGGGATAACATAAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCAAAGAGTTCAACGCGAATAACATTAGGGATACATTTCGGTTGCTGCTGCAAATGAGCGTTGTGCTTATGTTCGGAGGGCAGCTGCCGGTTGTGAAGgtatgaattcatcttaagctcctcaataagttgcgagggctcgctgctaggctcgatgaagcgtcaagagcggacggctgtaatttgtcgagcattttgtaatgtaatataacgttgtcgtcctaagtaatttgcagctcgcgatttaagattgggttttgaggaatgtgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC