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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttttaaatgattcgatttcgggtttttataaattttatcttcagaacctgtagaagaactatgt...

Basic information

species Physcomitrella patens
transcript PP1S42_100V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttttaaatgattcgatttcg-ggtttttataaattttatcttcagaacctgtagaagaactatgt----------
 || || || || || |||||||||||||| |||||||||||  ||||||| ||||| |  ||| | ||||||||||| |||||||| |||||||||||||||   |       ||||| | |   |||  |||||    ||||| ||   || |  | || ||  |  | |||| | |||  |   ||||    ||   |          
AAACGATATTCACATTGACATCATGGATTATATCTCACCTGCTACTTGTGCCGATGTTGCTTTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtagggt-------tctttctcaagcttcagcttttgc--aaatgcttgttttacaagattctttcatgtattatttgcag--ctgctagattttcttcttcactgtgatc

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttttaaatgattcgatttcg--ggtttttataaattttatcttcag-aacctgtagaagaac-tatgt---
 ||||| || || || |||||||||||||| |||||||| ||| |||| || |||||    ||| | ||||||||||| |||||||| |||||||||||||||    |  | ||    ||| | ||||       | ||  ||||| |  | || |  |  | ||||    |  |  ||  | |  || ||   |  | | |||   
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattt-------tgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttcccct-tttttttaaa---tgattcgatttcgggtttttataaattttatcttcagaacctgtagaagaactatgt
 ||||| || || |||||||||||||||||||||||||||||  | |||||||||||    ||| | ||||||||||| ||||||||||||||||| |||||||  |     ||| |   || || ||      | |  |||||   |  |    |||  | |   | | | | |    |  |     |  | ||    |    
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt----

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G011101_T01 (Zea mays), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccc---cttttttttaaatgattcgatttcgggtttttataaattttatcttcagaacctgtagaagaactatgt
 ||||| || || |||||||||||||||||||||||||||||  | ||||| |||||    ||| | ||||||||||| ||||||||||||||||| |||||||| |     ||| |   || || ||        ||| ||| |   |   | | |     | |       |||||  ||||    | ||  || || ||  
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACCTGTGCTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgcttctctgtacgttgcagttgtgaaatatttgtttcagcaaaatgttcttaaactgtagcctcctttatactcagt-tttatactagcac-ata-

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G392003_T01 (Zea mays), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttttaaatgattcgatttcgggtttttat---aaattttatcttcagaacctgtagaagaactatgt--
 |||||||| || || || || ||||||||||||||||||||  | ||||| ||||| |  ||| | ||||||||||| |||||||| |||||||| |||||||       | ||||| | |  ||||    ||| ||||  |||||    | |   |||||| |   |     ||||      || | ||  | |    |||  
AAATGACATTCACATTGATATTATGGATTACATCTCACCTGCTACATGTGCTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaata----gacctcttgtctg-attttttgtttgtttttcatgatggtttctgtagtttttgtcgcaggcactatcgcttacacttctaccatataggtgtaa

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G00610.1 (Glycine max), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttt---taaatgattcgatttcgggtttttataaatt-ttatcttcagaacctgtagaagaactatgt
 ||||| || ||||| ||||||||||| ||||| || |||||||||||||| ||||| |  |||||||  ||||||||||| ||||| |||||||||||||||          |||||| |  ||||  |  | |||||    ||| | |   |      | |  |||   || ||      || | ||  |     | |    
AAATGATATCCATATTGACATCATGGACTACATTTCTCCTGCATCTTGTGCCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctctttcctctttctcccattggctatgtttttaatcaaaaggtaaaaaaatatggtgctatcttttcttgctcaaagcaactccactttcatt----

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA08G23780.1 (Glycine max), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttt---taaatgattcgatttcgggtttttataaattttatcttcagaacctgtagaagaactatgt
 ||||| || ||||| ||||||||||| ||||| || |||||||||||||| ||||| |  |||||||  ||||||||||| ||||| |||||||||||||||          ||| || |  ||||  |  | |||||    ||| | |   |      | |  ||    |||| |   |  || |      |     ||  
AAATGATATCCATATTGACATCATGGACTACATTTCTCCTGCATCTTGTGCTGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatatctctttcctccttctctcattggctatgtttttaaccaaagggtaaaaaaatatggtgctacc--ttttcttgcccaaagcaaccccactttcatt-

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G31490.1 (Arabidopsis thaliana), 5'ss of exon 3
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttttaaatgattcgatttcgggtttttataaattttatcttcagaacctgtagaagaactatgt
 || |||||||| || || |||||||| || ||||| |||||    ||  |||| || |  |||||||  |||||||| || ||||||||||||||||||||||  |  | |   |||||  |  | |  |||| ||| |   |   |   ||     ||  |||||   ||  ||   | |    |      |      
TAACGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGCTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgtaatttaccgaaaccttttaaaagtattaccttctttgtttgtttgtttgttagattttggtataaccattgcctgttgtattattcatgtcag-----

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv09s0018g02080.t01 (Vitis vinifera), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgta---acctcacaatctcttttttacatttccccttttttttaaatgattcgatttcgggtttttataaattttatcttcagaacctgtagaagaactatgt
 |||||||| ||||| || || ||||||||||| || || ||||| ||||| ||||| |  || |||| |||||||||||| ||||| |||||||||||||||     |||| ||| | |  ||   | || |  |  | | |  ||   ||| | ||   |||    || |||      | |      ||  |  |  ||  
CAATGACATCCATATTGATATAATGGATTACATTTCTCCGGCATCCTGTGCTGATGTGGCATTTAGAACCATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtacgtctctcataatatttgcttcttaatttcaatactatatttattgatcggtctc---tttgagcaagtttcccagactgctttgataacatgaacatca

upper sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv04s0008g02320.t01 (Vitis vinifera), 5'ss of exon 2
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaa-cctcacaatctcttttttacatttccccttttttttaaatgattcgattt--cgggtttttataaattttatcttcagaacctgtagaagaactatgt
 |||||||| || || ||||||||||| ||||| || |||||   |||| | ||||| | ||||||||  |||||||| || ||||||||||||||||||||||  |    |       ||  |   ||  ||    |  |||   ||  ||| |   ||||  ||  ||  ||| | || | | | |  | |   | | |  
CAATGACATTCACATTGACATCATGGACTACATATCTCCTGCTGTTTGTACTGATGTGGCCTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgtaaatcatctagctgtccttccatgattttcccaaatggtaac--atctgatctaatgggtacttg-aatctttttgtttataccttacatagttatttttg

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|37826578|gb|BJ584590.1|BJ584590
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCCAAGACGTTCAAGAATTTCTGAACCATGT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATT-CAAGACGTTCAAGAATTTCTGAACCATGT
EST: gi|162172246|gb|FC348811.1|FC348811
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37823718|gb|BJ581784.1|BJ581784
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37841615|gb|BJ599623.1|BJ599623
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37848405|gb|BJ606413.1|BJ606413
EST:     CTGAATTNGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37842401|gb|BJ600409.1|BJ600409
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37827799|gb|BJ585811.1|BJ585811
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|18333783|gb|BJ165799.1|BJ165799
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37841943|gb|BJ599951.1|BJ599951
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCCAAGACGTTCAAGAATTTCTGAACCATGT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATT-CAAGACGTTCAAGAATTTCTGAACCATGT
EST: gi|162181484|gb|FC358098.1|FC358098
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|162272075|gb|FC447869.1|FC447869
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37832796|gb|BJ590808.1|BJ590808
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37846241|gb|BJ604249.1|BJ604249
EST:     CAGATGTCGTCTTCAGAAACATGTGGGNTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37829157|gb|BJ587169.1|BJ587169
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|37844982|gb|BJ602990.1|BJ602990
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
EST: gi|162185220|gb|FC361730.1|FC361730
EST:     CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAG                         GTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT
genomic: CAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTT

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

GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcac ... gcgtttgtagGTTGCTGTTAACACCAATATTCAAGACGTTCAAGAATTTCTGAACCATGTTGTTGCCTCAACTAATATGAAGTGCCTCACTCCTCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttttaaatgattcgatttcgggtttttataaattttatcttcagaacctgtagaagaactatgt

- - - - - - - - - - - - - - - - - - - - - - - - - CAGATG