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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattcagcgctctagtgttctgtttagcaaaaccctaaaccctaaacctcggtagatatcattttgatgaatttttggcaatttcgtatgcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGTACTAAAGAAGGGAGGAAAAGCGTGCCTCATCGGTCCTGTGCATCCTTCG

Basic information

species Physcomitrella patens
transcript PP1S47_21V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_21V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G082998_T01 (Zea mays), 3'ss of exon 1
gcattcagcgctctagtgttctgtttagcaaaaccctaa----accctaaacctcggtagatatcattttgatgaatttttggcaatttcgtatgcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGTACTAAAGAAGGGAGGAAAAGCGTGCCTCATCGGTCCTGTGCATCCTTCG
  ||| | |   |   || ||     | |||  |  ||     ||     | ||    |  || |   ||| ||| |||   ||  | || |     | |||||||| ||||||||||| ||||| ||||| || ||||  ||||||||||| || || |     || ||   ||| ||  | ||||| || ||  | ||  | 
-aattaatcatccccttgctcc--caaacaagccattagtatgacagctgagctacccaagta-cggattgctgattttcctgccctgtcatggtgctttgcagCATCGAGTACTGGCCAGACCCACAGCGGGGGATCAAGGAAGCCTACAGGGTCCTGAGATTTGGTGGGCTAGCTTGTGTGATCGGCCCGGTCTACCCGACC

upper sequence: PP1S47_21V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ09408 (Selaginella moellendorffii), 3'ss of exon 1
-gcattcagcgctctagtgttctgtttagcaaaaccctaaaccctaaacctcggtagatatcattttgatgaatttttggcaatttcgtatgcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGTACTAAAGAAGGGAGGAAAAGCGTGCCTCATCGGTCCTGTGCATCCTTCG
 | |||    |||   |  |    |  ||||     | |     ||   ||     |  |    | |||    |  | |  | |||| | |   | |||||||| ||||||||||||||||||||||| || ||||  || || ||| | || || ||||| || ||||| |||||| | |||||||| || || ||  | 
gggatttcctgctaacgcctgacttgaagcatgcatcaaggatttactgctaaacggtgaaaggtctgactt-tgatcgaaactttcttctttctctgcagCATAGAGTACTGGCCCGACCCTCAGCGAGGCATCAAAGAGGCGTACCGCGTGCTCAAGAAAGGTGGAAAGGCGTGCTTGATCGGTCCCGTCCACCCCACC

upper sequence: PP1S47_21V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ34610 (Selaginella moellendorffii), 3'ss of exon 1
gcattcagcgctctagtgttctgtttagcaaaaccctaaaccctaaacct--cggtagatatcattttgatgaatttttggcaa---tttcgtatgcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGTACTAAAGAAGGGAGGAAAAGCGTGCCTCATCGGTCCTGTGCATCCTTCG
     | |  ||    | | ||| | |    || |||  | |    |  |   | || |         |    | |||   | |   |||| | |   | |||||||| ||||||||||||||||||||||| || ||||  || |||||| | || || ||||| || ||||| |||||| | |||||||| || || ||  | 
-----ctgttctgggatttcctgctgacttgaagcctgcatcaaggatttactgctaaacggtgaaaggtctgactttgatcgaaactttcttctttctctgcagCATAGAGTACTGGCCCGACCCTCAGCGAGGCATCAAAGAGGCCTACCGCGTGCTCAAGAAAGGTGGAAAGGCGTGCTTGATCGGTCCCGTCCACCCCACC

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|208368737|gb|DC940004.1|DC940004
EST:     GACTTGCCCTTCAAGGCGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCA
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCA
EST: gi|162230436|gb|FC407091.1|FC407091
EST:     GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACT
EST: gi|100400394|gb|BY954455.1|BY954455
EST:     GACTTGCCCTTCANGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGTTATCACCGA-GCCTTCNGAGT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|208374173|gb|DC945219.1|DC945219
EST:     CCCTTCAAGACGGANTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
genomic: CCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|162270393|gb|FC447093.1|FC447093
EST:     GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|162230435|gb|FC407090.1|FC407090
EST:     GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAAT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|208358952|gb|DC946381.1|DC946381
EST:     GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|208360935|gb|DC954105.1|DC954105
EST:     GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|208372761|gb|DC952648.1|DC952648
EST:     GACTTGCCCTTCAAGGCGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|208360609|gb|DC957848.1|DC957848
EST:     GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|208358286|gb|DC930699.1|DC930699
EST:     GACTTGCCCTTCAAGACGAACTATGCTGACCGATACATTTCANCGG-AAN                         CATNGAGTACTGGCCCGACCCTCAGCG
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCG
EST: gi|208358177|gb|DC939373.1|DC939373
EST:     GACTTGCCCTTCAAGACGAACTATGCTGAC-GATACATTTCANCGGGAN-                         CATTGAGTACTGGCC
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCC
EST: gi|162270392|gb|FC447092.1|FC447092
EST:     CAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
genomic: CAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
EST: gi|7147971|gb|AW509893.1|AW509893
EST:     GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAG                         CATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT
genomic: GACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGT

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: 10

AGGAGAAAGCGCCCCTCAAGGACTGCAAGATCATCGAAGGAGATGCCGAGGACTTGCCCTTCAAGACGGACTATGCTGACCGATACATTTCAGCGGGAAGgtacgaccag ... gcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGTACTAAAGAAGGGAGGAAAAGCGTGCCTCATCGGTCCTGTGCATCCTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctcggtagatatcattttgatgaatttttggcaatttcgtatgcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGTACTAAAGAAGGGAGGAAAAGCGTGCCTCATCGGTCCTGTGCATCCTTCG
           atatcattttgatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattcagcgctctagtgttctgtttagcaaaaccctaaaccctaaacctcggtagatatcattttgatgaatttttggcaatttcgtatgcttgtgcagCATTGAGTACTGGCCCGACCCTCAGCGTGGTATCACCGAAGCCTACAGAGTACTAAAGAAGGGAGGAAAAGCGTGCCTCATCGGTCCTGTGCATCCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA