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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaatatctgggcttctcaatgcattagtacagaatttggtggagacattgatctttcaggggttattgaaatcaggaatgatcggcagcaagcatggcgtttggcctcatggtctgactagttccttgtactggattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTTTCGAAGACTCCACTTTACCAG

Basic information

species Physcomitrella patens
transcript PP1S1_526V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 5
gtatcaatatctgggcttctcaatgcattagtacagaatttggtggagacattgatctttcaggggttattgaaatcaggaatgatcggcagcaagcatggcgtttggcctcatggtctgactagttccttgtactggattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTTTCGAAGACTCCACTTTACCAG
|||||| ||| ||   | ||  |||| ||  |   || ||  ||||   |||    ||||     ||| ||| |           | |||      |||  | |||   || ||    |   | |||  |  |  || | | | ||||| ||||| || |||||| | ||||||||||| ||||| |||||||||||||||| |||   ||| | ||| || ||| ||
gtatcactatatga-ttcctttatgccttgtt---gagttcagtggctgcat----ctttt----gttgttgta-----------ttggc------catttcttttatgctaat----ttggtggtttttacttttgaaattttcagCTTGGAGCCAATGCTATTTTGGCAGTGTCACTTGCTGTCTGCAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 5
gtatcaatatctgggcttctcaatgcattagtacagaatttggtggagacattgatctttcaggggttattgaaatcaggaatgatcggcagcaagcatggcgtttggcctcatggtctgactagttccttgtactggattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTTTCGAAGACTCCACTTTACCAG
                        | || | ||     |||| | |     ||||  ||     ||| | || | ||     |   ||        |||    |||   || || |   |  |  |||    || || | | | ||||| ||||| || |||||| | ||||||||||| ||||| || ||||||||||||| |||   ||| | ||| || ||| ||
------------------------gtatcactatgttttttgtttgtcttgttgagttt-----ggtgactgca-tcttttgtagccg-tgttggccatccattttaagctaatcg---ggtt--ttcacaatattgaaattttcagCTTGGAGCTAATGCTATTTTGGCAGTGTCACTTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG
















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|18331408|gb|BJ163419.1|BJ163419
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|162255467|gb|FC431881.1|FC431881
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100361970|gb|BY947718.1|BY947718
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18328573|gb|BJ160578.1|BJ160578
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|162180206|gb|FC355523.1|FC355523
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18330497|gb|BJ162503.1|BJ162503
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|162275868|gb|FC451429.1|FC451429
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|162279243|gb|FC455790.1|FC455790
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18332103|gb|BJ164116.1|BJ164116
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAAC
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAAC
EST: gi|208374338|gb|DC941151.1|DC941151
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18344784|gb|BJ176825.1|BJ176825
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|162255274|gb|FC431584.1|FC431584
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18349793|gb|BJ181843.1|BJ181843
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCANTGTCACTGGCTGTGTGCAANGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|18331257|gb|BJ163266.1|BJ163266
EST:     TTCACGAGCTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100361603|gb|BY966133.1|BY966133
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|162255040|gb|FC430913.1|FC430913
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|100352733|gb|BY945421.1|BY945421
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
EST: gi|162186412|gb|FC362968.1|FC362968
EST:     TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAG                         CTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT
genomic: TTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGT

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: 99

GACCCCACAAACCAAACTGCAATCGACAACTTCATGGTTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatcaatat ... gattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTTTCGAAGACTCCACTTTACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagcatggcgtttggcctcatggtctgactagttccttgtactggattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTTTCGAAGACTCCACTTTACCAG
                       gtctgac  putative branch site (score: 99)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcaatatctgggcttctcaatgcattagtacagaatttggtggagacattgatctttcaggggttattgaaatcaggaatgatcggcagcaagcatggcgtttggcctcatggtctgactagttccttgtactggattgtgcagCTGGGAGCGAACGCTATTCTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTTTCGAAGACTCCACTTTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA