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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGTTTGATGGTCAGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttcagtctatgtaattaatattggcgcagatcgagttctttgattctacggtttgtgtttgtcggtgaaactgagatttggtcgtatctgtca...

Basic information

species Physcomitrella patens
transcript PP1S215_28V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S215_28V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT1G23310.2 (Arabidopsis thaliana), 5'ss of exon 11
ATGGGTTTGATGGTCAGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgt-tcagtctatgtaattaatattggcgcagatcgagttctt--tgattctacggtttgtgtttgtcggtgaaactgagatttggtcgtatctgtca
|||||||||||||| | ||||||||| || ||||||||||| |||   | || |      ||||||||    | | ||  ||  |  |    ||   |     | || |   |    | ||  |  ||||    | ||  |                           
ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAGTTCGCCCGTGAAAGgtatatatataagcttacatgctcgtgatcatcatccctggattgaataacaaatcgcccttttgcacatttctttag-------------------------
















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|162177268|gb|FC353425.1|FC353425
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162151905|gb|FC328151.1|FC328151
EST:     TCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: TCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162153917|gb|FC329424.1|FC329424
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162217936|gb|FC393932.1|FC393932
EST:     GTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: GTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162186626|gb|FC363598.1|FC363598
EST:     GTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: GTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|37824967|gb|BJ583033.1|BJ583033
EST:     AGTCNTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162178884|gb|FC354816.1|FC354816
EST:     TGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: TGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162186047|gb|FC361875.1|FC361875
EST:     TGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: TGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162207831|gb|FC384124.1|FC384124
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162178100|gb|FC354402.1|FC354402
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162177755|gb|FC354589.1|FC354589
EST:     TCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: TCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162188179|gb|FC363945.1|FC363945
EST:     CTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: CTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162269856|gb|FC445386.1|FC445386
EST:     CCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: CCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162214586|gb|FC390617.1|FC390617
EST:     CCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: CCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162178885|gb|FC354817.1|FC354817
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162188180|gb|FC363946.1|FC363946
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162179082|gb|FC356483.1|FC356483
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAAGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162186162|gb|FC361366.1|FC361366
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162189252|gb|FC366748.1|FC366748
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162189251|gb|FC366747.1|FC366747
EST:     TCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: TCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162253479|gb|FC430113.1|FC430113
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162269857|gb|FC445387.1|FC445387
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162253480|gb|FC430114.1|FC430114
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162217937|gb|FC393933.1|FC393933
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162151637|gb|FC327766.1|FC327766
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162155909|gb|FC332458.1|FC332458
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|162181981|gb|FC356852.1|FC356852
EST:     TCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTCTNTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: TCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG
EST: gi|208376494|gb|DC922525.1|DC922525
EST:     AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG                         TGAAGCTATCTCGCTGTC-TTGAGGAAAAGAGCGCATATCATGACAGATGG
genomic: AGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGG

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: 32 (upstream exon), 35 (downstream exon)
Score: 9

ATGGGTTTGATGGTCAGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttc ... tatattgcagTGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGTTTGATGGTCAGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAGgtacccgttcagtctatgtaattaatattggcgcagatcgagttctttgattctacggtttgtgtttgtcggtgaaactgagatttggtcgtatctgtca

- - - - - - - - - - - - - -  AGGAGA