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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGCCTCTGATATTGTGCTCACCGAACCTGGTCTCAGTGTCATTATAAGTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgtttttttgatataaatttggtttctgtttagatggatacgtgtccttgcactcgggatccattcatgtgtgtgttggtgaggcagtatccagcaa...

Basic information

species Physcomitrella patens
transcript PP1S6_11V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_11V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ07042 (Selaginella moellendorffii), 5'ss of exon 14
GAGTGCCTCTGATATTGTGCTCACCGAACCTGGTCTCAGTGTCATTATAAGTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgtttttttgatataaatttggtttctgtttagatggatacgtgtccttgcactcgggatccattcatgtgtgtgttggtgaggcagtatccagcaa
|||||| ||||||||||| || || || || || || ||||| ||||| ||||||||  | |||||||| || || |||||||| ||||| |||||||||||  |     |||  |    |||  ||    | || |     |  ||||    ||                                             
GAGTGCATCTGATATTGTTCTAACTGAGCCCGGCCTTAGTGTGATTATCAGTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcgttgcaacgtctttacttc---tctaaactataagctgtctccacag--------------------------------------------
















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|162193951|gb|FC371764.1|FC371764
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162198821|gb|FC374304.1|FC374304
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162174468|gb|FC350747.1|FC350747
EST:     TGCTGTGTTGACCAGCCGAAGCA-TTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: TGCTGTGTTGACCAGCCGA-GCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162252827|gb|FC428858.1|FC428858
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162267612|gb|FC444675.1|FC444675
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162185478|gb|FC362560.1|FC362560
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162198374|gb|FC375547.1|FC375547
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|100379616|gb|BY949858.1|BY949858
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162183362|gb|FC359277.1|FC359277
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162184822|gb|FC361124.1|FC361124
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162186679|gb|FC363651.1|FC363651
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTGCTT
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTGCTT
EST: gi|162179356|gb|FC356305.1|FC356305
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162176072|gb|FC351866.1|FC351866
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162159442|gb|FC336231.1|FC336231
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162178407|gb|FC354131.1|FC354131
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162183465|gb|FC359588.1|FC359588
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTGC
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTGC
EST: gi|162198177|gb|FC375480.1|FC375480
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162197978|gb|FC373993.1|FC373993
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162168958|gb|FC345640.1|FC345640
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162153187|gb|FC329593.1|FC329593
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162185798|gb|FC362354.1|FC362354
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG
EST: gi|162163564|gb|FC339474.1|FC339474
EST:     GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACG                         ATCTACGCTGTTTCTATCACCATCCGTATCGTG
genomic: GTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG

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: 30 (upstream exon), 24 (downstream exon)
Score: 11

GAGTGCCTCTGATATTGTGCTCACCGAACCTGGTCTCAGTGTCATTATAAGTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgttttt ... gtatctgcagATCTACGCTGTTTCTATCACCATCCGTATCGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGCCTCTGATATTGTGCTCACCGAACCTGGTCTCAGTGTCATTATAAGTGCTGTGTTGACCAGCCGAGCAATTTTCCAGCGCATGAAGAACTACACGgtttgtttttttgatataaatttggtttctgtttagatggatacgtgtccttgcactcgggatccattcatgtgtgtgttggtgaggcagtatccagcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC