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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGCGGATGTGAAGTACATCGATCCTACGTACATGATCCGAGCCTGTCGAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttctctctgggacagacataggtcaatacaaaatatctatcatacataacatatgttctgttattcatctgtaggaatcacgattcgtcgacaagttcaattctcttctacagggtttctgatttgaatctttccgttttttggaaactgctttgtatacag

Basic information

species Physcomitrella patens
transcript PP1S94_106V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S94_106V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA01G03040.1 (Glycine max), 5'ss of exon 12
AGCA-GCGGATGTGAAGTACATCGATCCTACGTACATGATCCGAGCCTGTCGAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttctctctgggacagacataggtcaatacaaaatatctatcatacataacatatgttctgttattcatctgtaggaatcacgattcgtcgacaagttcaattctcttctacagggtttctgatttgaatctttccgttttttggaaactgctttgtatacag
  || || || || || || |||||||| |||||||||||||| || |||||||| |||||||||||  |||| || ||  |||||||||| || || || ||  |||| |||||     |   |||    |  |     |||| ||| ||         |  || |||||||  |    |       |  ||  | | |   ||  ||||||                                                         
-TCATGCTGACGTTAAATATATCGATCCAACGTACATGATCCGTGCATGTCGAGCAAATGCTTCTGATGGAATTTTATGCACTGTACTTGGACAAAATGCTgttagtct-ctctccttctctatcattttcc--tgttgcatatatatgattt------cactttttgttattgtttctcatagg---cagtttattggcc--ttttattctcaa-------------------------------------------------------
















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|67693514|gb|BJ953747.1|BJ953747
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|162203811|gb|FC379908.1|FC379908
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|37852524|gb|BJ610532.1|BJ610532
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|7648346|gb|AW739329.1|AW739329
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|18336359|gb|BJ168381.1|BJ168381
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACCTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|162229043|gb|FC404753.1|FC404753
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|67697835|gb|BJ958068.1|BJ958068
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|162198099|gb|FC372126.1|FC372126
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|37824275|gb|BJ582341.1|BJ582341
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|37850516|gb|BJ608524.1|BJ608524
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|7648257|gb|AW739240.1|AW739240
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|162229044|gb|FC404754.1|FC404754
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC

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: 27 (upstream exon), 35 (downstream exon)
Score: 7

AGCAGCGGATGTGAAGTACATCGATCCTACGTACATGATCCGAGCCTGTCGAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAACAATCATTATGTTCTATTACCCATCCCAGAGGTGATTGCCTACGCAAGAA




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