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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggtcccaagatgtaattcttgattgcataaatactcgtttacgagcgtattcttgtttgtcttcttaatgagatctaagaaggttaacttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGTGTAGGTGCCATCCGAAATGCCCTCGATTTAGCAGGATACCACGATGTTT

Basic information

species Physcomitrella patens
transcript PP1S450_21V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S450_21V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 8
caggtcccaagatgtaattcttgattgcataaatactcgtttacgagcgtattcttgtttgtcttcttaatgagatctaagaagg----ttaacttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGTGTAGGTGCCATCCGAAATGCCCTCGATTTAGCAGGATACCACGATGTTT
    |    | || |  || |   || |  |  |    | || |     ||  ||| | | |      | | | || |     |     |||| ||      |||| |||||||| |||||||||||||| |||||||||||||||||||| || ||||| ||  | ||    || || |||   | ||| |  ||  ||||||
----tgaggaaatatgcttttatgttcccgatctctaaggtttccttgctacacttctctataacaccactaacattttttttgtctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT

upper sequence: PP1S450_21V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA06G12110.1 (Glycine max), 3'ss of exon 7
caggtcccaagatgtaattcttgattgcataaatactcgtttacgagcgtattcttgtttgtcttcttaatgagatctaagaaggtt-aacttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGTGTAGGTGCCATCCGAAATGCCCTCGATTTAGCAGGATACCACGATGTTT
 |  ||   | |||   || |       |||  ||    ||         | |||   |        |||     | |  |    || || ||      |||| |||||||| |||||||||||||| |||||||||||||||||||| || ||||| ||  | ||    || || |||   | ||| |  ||  ||||||
-aaatcatcatatgcttttatgttcccaatatctaaagtttccttgctacactctctataacaccactaacattttttttgtctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTTGATGCTGAAGGCTTTCAGCATGTTT
















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|208357191|gb|DC926538.1|DC926538
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162234870|gb|FC410643.1|FC410643
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162218487|gb|FC395064.1|FC395064
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|208353431|gb|DC918487.1|DC918487
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162234869|gb|FC410642.1|FC410642
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|37828958|gb|BJ586970.1|BJ586970
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCNTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|100379688|gb|BY949894.1|BY949894
EST:     ATGAACGACGAGACAGTTTCATCA-CTTTTGCA-GCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: ATGAACGACGAGACAGTT-CATCAACTTT-GCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|37852710|gb|BJ610718.1|BJ610718
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162268622|gb|FC443676.1|FC443676
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162227018|gb|FC403362.1|FC403362
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162184165|gb|FC359639.1|FC359639
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162176322|gb|FC353507.1|FC353507
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|208397366|gb|DC916320.1|DC916320
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|37827165|gb|BJ585177.1|BJ585177
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|208380828|gb|DC923310.1|DC923310
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|67727441|gb|BJ977700.1|BJ977700
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162265940|gb|FC442943.1|FC442943
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|208388243|gb|DC945575.1|DC945575
EST:     TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|37821562|gb|BJ579628.1|BJ579628
EST:     AACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: AACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
EST: gi|162227004|gb|FC403361.1|FC403361
EST:     TGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG                         GCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT
genomic: TGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGT

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: 28 (upstream exon), 28 (downstream exon)
Score: 6

GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAGgtacaggatt ... ttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGTGTAGGTGCCATCCGAAATGCCCTCGATTTAGCAGGATACCACGATGTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgtattcttgtttgtcttcttaatgagatctaagaaggttaacttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGTGTAGGTGCCATCCGAAATGCCCTCGATTTAGCAGGATACCACGATGTTT
                  ttcttaat  TA-rich tract