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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcccttggtttttctcttagaccagtgaacaccgttttactcacgaccagtcttgtcagtgtatgcaattgggccttcacatcacatgaagtgcaacatttgcagtgtcattgtgccgtacaatttcgatttgtagttcttatcgagcctaatgaattgtattttgtcactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTGCTAGTGACATTCAGTAACGATAACACAATGAAACTTTGGAAACCGTGAA

Basic information

species Physcomitrella patens
transcript PP1S31_68V6.1
intron # 15
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|37829082|gb|BJ587094.1|BJ587094
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|67696983|gb|BJ957216.1|BJ957216
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|208354419|gb|DC953825.1|DC953825
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|37833181|gb|BJ591193.1|BJ591193
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGGCAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|67726106|gb|BJ976365.1|BJ976365
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|208347871|gb|DC917592.1|DC917592
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|208400522|gb|DC925272.1|DC925272
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|37834363|gb|BJ592375.1|BJ592375
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|37840113|gb|BJ598121.1|BJ598121
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
EST: gi|208399731|gb|DC924929.1|DC924929
EST:     ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACG                         GCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG
genomic: ATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTG

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: 25 (upstream exon), 35 (downstream exon)
Score: 5

AAATATCTACTGCTTTAGTCATCAATCAGGCAAGCTTGAACACTTGATGACGgtaagttctc ... cactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTGCTAGTGACATTCAGTAACGATAACACAATGAAACTTTGGAAACCGTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcgatttgtagttcttatcgagcctaatgaattgtattttgtcactcgacagGCTCACGACAAGGATATTATTGGAGTGACGCACCATCCTCATCGTAATTTGCTAGTGACATTCAGTAACGATAACACAATGAAACTTTGGAAACCGTGAA
                        gcctaat  putative branch site (score: 5)
                                       ttttgtc  putative PPT
                           taatgaattgtatttt  TA-rich tract