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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattggatttttctcctatttcgagtgatctcactgattgagaaagatgtgaagggggtaagcattgttgacaattgtgacttgttttcaaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCGAGCACCAAATTTTAGTTCCGACATTGTCTGTCCTGAAACTTTCTGAGAG

Basic information

species Physcomitrella patens
transcript PP1S4_75V6.1
intron # 1
splice site 3'
intron type U2

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|67572953|gb|BJ945777.1|BJ945777
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162223589|gb|FC399713.1|FC399713
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|18351485|gb|BJ183537.1|BJ183537
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|18365447|gb|BJ197523.1|BJ197523
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162172794|gb|FC348383.1|FC348383
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162249183|gb|FC421227.1|FC421227
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|67696335|gb|BJ956568.1|BJ956568
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162209382|gb|FC385497.1|FC385497
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162209383|gb|FC385498.1|FC385498
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162235543|gb|FC411340.1|FC411340
EST:     CGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: CGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162235544|gb|FC411341.1|FC411341
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162271170|gb|FC447159.1|FC447159
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162223590|gb|FC399714.1|FC399714
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162259933|gb|FC435236.1|FC435236
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|18362341|gb|BJ194411.1|BJ194411
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162210449|gb|FC386537.1|FC386537
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|19778834|gb|BQ039368.1|BQ039368
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162228470|gb|FC404120.1|FC404120
EST:     GCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: GCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|67578157|gb|BJ950324.1|BJ950324
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162259934|gb|FC435237.1|FC435237
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|67698062|gb|BJ958295.1|BJ958295
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|100444457|gb|BY964155.1|BY964155
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162271171|gb|FC447160.1|FC447160
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162245153|gb|FC421601.1|FC421601
EST:     GCCAACGGCGACATGCTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: GCCAACGGCGACATG-TTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162213088|gb|FC389512.1|FC389512
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|162258993|gb|FC435936.1|FC435936
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
EST: gi|67574646|gb|BJ947470.1|BJ947470
EST:     AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAG                         GAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG
genomic: AGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCG

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), 34 (downstream exon)
Score: 57

GCTGTTGCTGTTGGGAGGAAGAGATGCGCTGGGGAGAGGTTGATGGTGCGAGCCAACGGCGACATGTTGGGTGATTTCGGAGCTCGTGACCCTACCGCAGgtcagaaatc ... aaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCGAGCACCAAATTTTAGTTCCGACATTGTCTGTCCTGAAACTTTCTGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtgaagggggtaagcattgttgacaattgtgacttgttttcaaatcctcagGAGAACTAGGAAGCAACTTTGGGGAGAAGACGTTAGGTAATGCGTCTACCGAGCACCAAATTTTAGTTCCGACATTGTCTGTCCTGAAACTTTCTGAGAG
                     tgttgac  putative branch site (score: 57)
                                                tcctc  putative PPT
                                        ttttcaaat  TA-rich tract