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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttacctcctaagtatgagatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG

Basic information

species Physcomitrella patens
transcript PP1S280_23V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os07g48300.1 (Oryza sativa), 3'ss of exon 8
------------------------------------------------------------------atttttacctcctaagtatga-gatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG
                                                                    |  ||  |  || || ||  | |  | ||||| || || |   || |  | | |    |  ||  |  |    |||| ||||  ||       || |||| ||||||||||| |||||||||||||| ||||||||||||||||| |||||||| ||||| |||||||||||||| || ||||||
gtaagttatcctacttcattcccttggttgaacagatgagcttcccctttttcatgtgtggtaaactatcataagttgtacgtttgttgtttactgttttgttagtgttagttgacttaagatttcaagggttatatgcaactta-ttgcgtctttaaacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG

upper sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 8
atttttacctcctaagtatgagatcgcagttttttttgtatacctttatctgaaaag--gaagtggaaaggttat-tcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG
   ||||    ||   |        |  ||  | | |||     | |   | ||     |  |||  ||  |||  || |  ||  |  | | |   || |||| ||||| ||||| |||||||| |||||||| ||||||||||| ||||| ||||||||| || |||||||||||||||| ||||||
--gtttattctcttgttccttttatgaggtcctatgtgtgggattgtcattaaagtcttgttgtgctaaacttacatccttttttaatttcactccttt-cagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG

upper sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G080048_T01 (Zea mays), 3'ss of exon 7
----------------------------------------atttttacctcctaagt--atgagatcgcagttttttttgtatacctttatctgaa-aaggaagtggaaaggttatt----------cttacttgcacctga--------ttgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG
                                         |||||   |  | |    ||||  |   |   |  ||  | |    | || |||   |  || |   | |||| ||          ||  ||   | ||||        |  | |  |||| ||||||||||| |||||||| ||||||||||||||||||||||| |||||||| ||||| |||||||||||||| || ||||||
gtaagttatccaatttgatcgcgttgatacttgtagtatgcttttttttttttgaacagatgatgttataagctacttgctgtttgctgatatgattgaataaatatgatggttgtttattgtttttctccctgctatctgaaagttgactcatttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG

upper sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G030646_T02 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------atttttacctcctaagtatga-----gatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttac----ttgcacctgattg--tgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG
                                                               |||    |  |||| ||       | | ||  || |  ||| |||  | |   || |    |  |        | | |   |    |   || ||| ||  | |  |||| ||||| ||||| |||||||| ||||||||||||||||| ||| | ||||| || ||||| |||||||||||||| || ||||||
gtaagctatccattttgattgcgttgatatttgtagtatgcctttttggatatatggtgctgctttccttttataagcatacttgctgtttgctattatgattgaataaatatgattgtagtttaccttttttctctctccccgcgatctgaaacttgactgaatttcacagATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG

upper sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 7
atttttacctcctaagtatgagatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttacttgcacctgatt--gtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG
||    |    | |   |   | |      ||||||  | |   ||||| |  ||      |  | |  |  | |||  ||       |||  |  ||  ||| || || ||||| ||||||||||||||||| || |||||||||||||| || |||||  || |||||||||| || || || |||
atgcggagaatcaacacaaatgtttttcaattttttaatgt--ttttatttctaagcttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG

upper sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ28838 (Selaginella moellendorffii), 3'ss of exon 7
atttttacctcctaagtatgagatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG
                  | || || || | | ||||   | ||||  | |     |     ||| |  | |||  |         | || |  | ||||| || ||||| ||||||||||| ||||||||||| || || |||||||| || || ||  |||| || || || || || || || 
-----------------gtaagttctcaatctcttttcatttccttcgtttcgtttgtcta-ggagaaatcatttct---------ttatcg-atcgcagATGAATACGTTATGTGCAATGGCTGCAAGAGCCCCGACACTATTCTTTCGAAAGAAAACAGGCTCTTTTTTCTACGATGCGAGCAA

upper sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ17507 (Selaginella moellendorffii), 3'ss of exon 3
atttttacctcctaagtatgagatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG
                  | || || || | | ||||   | ||||  | |           ||| |  | |||  |         | || |  | ||||| || ||||| ||||||||||| ||||||||||| || || |||||||| || || || ||||| || || || || || || || 
-----------------gtaagttctcaatctcttttcatttccttcgtttcgtttatcta-ggagaaatcatttct---------ttatcg-atcgcagATGAATACGTTATGTGCAATGGCTGCAAGAGCCCCGACACTATTCTTTCGAAAGAAAACCGGCTCTTTTTTCTACGATGCGAGCAA

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|37838318|gb|BJ596326.1|BJ596326
EST:     AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCA                         ACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
genomic: AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCAgtaagattct ... tgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
EST: gi|37837355|gb|BJ595363.1|BJ595363
EST:     AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCA                         ACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
genomic: AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCAgtaagattct ... tgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
EST: gi|37824018|gb|BJ582084.1|BJ582084
EST:     AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCA                         ACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
genomic: AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCAgtaagattct ... tgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
EST: gi|162238808|gb|FC417637.1|FC417637
EST:     AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCA                         ACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
genomic: AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCAgtaagattct ... tgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
EST: gi|162177655|gb|FC353241.1|FC353241
EST:     AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCA                         ACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA
genomic: AGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCAgtaagattct ... tgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCA

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: 33

GAGTTGGGTACTAGTGGATCACTCGATGGACAACAGCGTCTTGTTGTGAAAGGGCGATTTGCTCCCAAGGTGTTCGAGGGTATTCTGAGGCGCTACGTCAgtaagattct ... tgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctgaaaaggaagtggaaaggttattcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG
                        ttattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttacctcctaagtatgagatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT