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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagactactcagctcatctgaaacaaatgtgtagaaatg...

Basic information

species Physcomitrella patens
transcript PP1S331_37V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 5'ss of exon 3
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagactactca--gctcatctgaaacaaatgtgtagaaatg------------------------------------------------------------------------------
|||||| ||||    | | || || || || || || || || || | |||| | |||||||||||||| |||||||||||||| || || || |||| |||| |  ||   |  ||| ||  || | | |    ||| |   |    ||  |||||  ||  |    || |  |  |||||   |||  ||  |    |||                                                                              
CCACCCAACTGAAAAGAGGGACCTGTATGATGCTGATCATGGGAAAAAGGTGTTGAGCATGGCTCCTGGGCTTGAGAAGCTCAATATCCTTCCTTTCAAGgta-tgtcatcctaccagaccagatatcacat---tttttggatgcactagattgtgtagttcgctagcttactgtccatcttgtacatttgaatttggatgtcaagcaacatattttagttttcagataaaccttgttgtattctttttcttggcatgactcctgatttgttttatcag

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 3
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccagaatgacagcccctatctgat-aaatgtttctctgtc---gtttatgttgtgc-tgtgagactactcagctcatctgaaacaaatgtgtagaaatg------
||||||||| |      | || ||||| || || || |||||||||| |||  | |||||||||||||||||||||| ||||||||| || || |||| ||||         || ||   |||||||||  | || ||| ||| ||   |  ||||  |||  |   | || ||  |   ||  | | |      || | |  |       
CCACCCCACAGAGAAAAGGGACCTCTATGATGCTGATCACGGAAAGAAGGTTTTGAGCATGGCTCCTGGCCTTGAGAGGCTCAACATCCTTCCTTTCAAGgta---------tgtca--tcctatctgaccagatttttttctttccatgcatatgcagtgagtagaaaacaacatattgcaattaacattttgctgcacatctttacaca

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G158147_T01 (Zea mays), 5'ss of exon 3
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagactactcagctcatctgaa-acaaatgtgtagaaatg---------
 || || || |    | | ||  | ||| || |||| ||||| |||| ||| || ||||||||||||||  | ||||| |||||||| |||||||||| |||| ||   || | |||  |  |  |      ||||  |  |||| | |   |||   |||    | | ||| | ||| || |  || || |  ||   |          
ACATCCAACAGAAAAGAGGGACTTGTACAACCCAGATCACGGGAAGAAGGTCCTGAGCATGGCTCCTGGTTTAGAGAAACTCAACATACTGCCCTTCAAGgtattt---gattcacatacatttcc------atgtgacattgtcctattcattgaaatgtccagc-agtcaccgcatgtggatgcacattttgagcggtcacagtaccc

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 4
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaat---tccagaatgacagcccctatctgataaatgtttctctgtcgttta------tgttgtgctgtgag-actactcagctcatctgaaacaaatgtgtagaaatg------------------------------------------------------------------------------------
||| ||||| |      | || ||||| || || |||||||| |||| |||  | ||||||||||||||||| |||| ||||||||| || || |||| ||||     |||    ||||     || |    |  |||    ||    |  ||       ||  |||  | || | |  ||  | ||||| | ||| ||||  |    ||                                                                                    
CCATCCCACGGAGAAAAGGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgaccagatctcttccttccatgcacatccagtgagtaaaagaacgtattgcaatcagcatttttcttcacatct-atacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgttttcttgacatttttcttgtctgttattccggatcag

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G302080_T01 (Zea mays), 5'ss of exon 10
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaat---tccagaatgacagcccctatctgataaatgtttctctgtcgttta------tgttgtgctgtgag-actactcagctcatctgaaacaaatgtgtagaaatg------------------------------------------------------------------------------------
||| ||||| |        || ||||| || || |||||||| |||| |||  | ||||||||||||||||| |||| ||||||||| || || |||| ||||     |||    ||||     || |    |  |||    ||    |  ||       ||  |||  | || | |  ||  | ||||| | ||| ||||  |    ||                                                                                    
CCATCCCACGGAGAAAATGGACCTCTATGATGCTGACCACGGGAAGAAGGTTTTGAGCATGGCTCCTGGCCTCGAGAGGCTCAACATCCTTCCTTTCAAGgtatgccatccttcctgaccagatctcttccttccatgcacatccagtgagtaaaagaacgtattgcaattagcatttttcttcacatct-atacacatgtcaatctttgatgttttttagttatcaagaaaatagaaagatttattgtttgtctgctttcttgacatttttcttgtctcttattctggatcag

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA13G06940.1 (Glycine max), 5'ss of exon 3
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaatt----ccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagactactcagctcatctgaaacaaatgtgtagaaatg
|||||| ||||      | ||| | || ||| | || || ||||||| |||||| ||||||||||| || || |||||||| |||||| |||| |||||||||| |      |   | |||       |  | |   || | ||||||    |||||| |  |   |  |||     ||||         | ||  ||      
CCACCCAACTGAGAAAAGGGATTTGTATGACCCTGATCATGGAAAGAAGGTGCTTAGCATGGCTCCCGGTCTGGAGAAGCTTAACATTTTGCCATTCAGGgtaagtagtattactttaacatatggctttaggttcttgctcctctgtgagatatgttct--ttcaatgctatcttcctcacaatgttttactgcatattgt--

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA19G05020.1 (Glycine max), 5'ss of exon 4
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccagaatgacagcccctatctgataaatgtttctctgtcgtttatgt--tgtgctgtgagactactcagctcatctgaaacaaatgtgtagaaatg-
|||||| ||||      | ||| | || ||| | || || ||||||| ||| |||| |||||||||||| || |||||||| |||||| |||| ||||| |||| |  || || ||     | || ||   |  | ||||   || | | ||   | || | |   | | ||    || ||  ||     |   |   | || 
CCACCCAACTGAGAAAAGGGATTTGTATGACCCTGATCATGGAAAGAAGGTACTCAACATGGCTCCTGGTCTGGAGAAGCTTAACATTTTGCCATTCAGAgtaagt--agtattactttaac-atatggctataggttcttgctcctctgtgagatatgttctttcaatgctatcttcctcacaatgttttacttcatattgt

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv18s0001g14010.t01 (Vitis vinifera), 5'ss of exon 3
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagac-tactcagctcatctgaaacaaatgtgtagaaatg
 ||||| || |    | | ||| | || ||| | ||||| || || | |||| | ||||||||||||||| | |||||||| || |||||||| |||||||||  |      ||| | | |   ||| |   ||||||        ||||  |   | | |      |  ||   |||    |      ||  |  |   |
TCACCCAACAGAGAAGAGGGATTTGTATGACCCTGACCATGGGAAAAAGGTGTTAAGCATGGCTCCTGGCTTGGAGAAGCTAAATATTCTGCCATTCAGGgtaggtttttcttgata-ctctgctctcacccatgtttgctcaagttttaattcaggttatattgtatcttcttttcacaaaatttccctgcatctagtag

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ32830 (Selaginella moellendorffii), 5'ss of exon 3
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaa--ttccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagactactcagctcatctgaaacaaatgtgtagaaatg
 ||||||| ||     || ||||| || ||||| |||||||| ||| |||| |||||||||||||||||  | |||    | ||||| || || ||||||||||  ||||    ||   |    |  | || |      |||   ||  || | || ||   | ||                                    
ACACCCCATTGAAAAACGTGATCTGTATGACGCGGACCACGGGAAGCTGGTTCTCAGCATGGCTCCTGGATTGGAGCGCTTGAACATCCTTCCTTTCAGGgtaacgttcctttgtgctcgtgagttgcggaaactaacatcttgttcacttctcttttggattcag------------------------------------

upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ22935 (Selaginella moellendorffii), 5'ss of exon 3
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaa--ttccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagactactcagctcatctgaaacaaatgtgtagaaatg
 ||||||| ||     || ||||| || ||||| |||||||| ||| |||| |||||||||||||||||  | |||    | ||||| || || ||||||||||  ||||    ||   |    |  | || |    | |||   ||  || | || ||   | ||                                    
ACACCCCATTGAAAAACGTGATCTGTATGACGCGGACCACGGGAAGCTGGTTCTCAGCATGGCTCCTGGATTGGAGCGCTTGAACATCCTTCCTTTCAGGgtaacgttcctttgtgctcgtgagttgcggaaactaatatcttgttcacttctcttttggattcag------------------------------------

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|162162006|gb|FC338589.1|FC338589
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37849069|gb|BJ607077.1|BJ607077
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|162176154|gb|FC351090.1|FC351090
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37853261|gb|BJ611269.1|BJ611269
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37848002|gb|BJ606010.1|BJ606010
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37850021|gb|BJ608029.1|BJ608029
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|67691750|gb|BJ951983.1|BJ951983
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|208372292|gb|DC948481.1|DC948481
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37821007|gb|BJ579073.1|BJ579073
EST:     TGCTCAGCATGGCTCNTGNCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37850056|gb|BJ608064.1|BJ608064
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|162176153|gb|FC351089.1|FC351089
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37822990|gb|BJ581056.1|BJ581056
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC

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: 31 (upstream exon), 35 (downstream exon)
Score: 30

CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCCAGGGCGCAGGACTTTTTGTTCATTTCTGGTACCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccagaatgacagcccctatctgataaatgtttctctgtcgtttatgttgtgctgtgagactactcagctcatctgaaacaaatgtgtagaaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaat