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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacccgaatctctctcctgaaaagcactctcctcttgtctgttacgccattatccctcaactagctcttacttgtacagcgacagtgtttacagaatagatagcactcactagccaagggaaacgtatcatcgcgagagagaattgcgtgctgaaccatcacctctggggtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGACAGGCACTGCGAAACCGGAGGCTGTCCTGAAGACCGCACAGAAGATGAA

Basic information

species Physcomitrella patens
transcript PP1S494_6V6.1
intron # 3
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|208346409|gb|DC912802.1|DC912802
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|100356224|gb|BY946257.1|BY946257
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|18352926|gb|BJ184981.1|BJ184981
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCANAANCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|100369626|gb|BY948572.1|BY948572
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|100355300|gb|BY965092.1|BY965092
EST:     TGCGAAAAGTGTGCCCGCAAAATGAGCNNNNNNNCTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: TGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAA-CTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|162219181|gb|FC396620.1|FC396620
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|100387241|gb|BY970385.1|BY970385
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|162219180|gb|FC396619.1|FC396619
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|100397749|gb|BY990381.1|BY990381
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|100408559|gb|BY974187.1|BY974187
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|37834364|gb|BJ592376.1|BJ592376
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|7583880|gb|AW699782.1|AW699782
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|7584234|gb|AW700131.1|AW700131
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|7583899|gb|AW699801.1|AW699801
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
EST: gi|100446956|gb|CJ971255.1|CJ971255
EST:     CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATG                         GTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA
genomic: CTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGA

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: 34 (upstream exon), 35 (downstream exon)
Score: 30

ACAATCGAATTAAAGGTACACCTATGCTGCGAAAAGTGTGCCCGCAAAATGAGCAAAAAACTCGAGAGTATGGATGgtgagtaccc ... gtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGACAGGCACTGCGAAACCGGAGGCTGTCCTGAAGACCGCACAGAAGATGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacccgaatctctctcctgaaaagcactctcctcttgtctgttacgccattatccctcaactagctcttacttgtacagcgacagtgtttacagaatagatagcactcactagccaagggaaacgtatcatcgcgagagagaattgcgtgctgaaccatcacctctggggtatacgcagGTGTGCAGAAGCCTGTGATTTGCGACCTGTACCTGACGAAGGTGACAGTGACAGGCACTGCGAAACCGGAGGCTGTCCTGAAGACCGCACAGAAGATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG