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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCTCAAGTTCCAGCGCAACTTGCGTTCTGTTGCGGAGGAGCGGGCAGGAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaaacatcttggctcttacatgggttccgcccattctgagcactggctactcatttcggttaagggtttagggtttaaggttctatttttgtg...

Basic information

species Physcomitrella patens
transcript PP1S68_114V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G084757_T02 (Zea mays), 5'ss of exon 2
GCAGCTCAAGTTCCAGCGCAACTTGCGTTCTGTTGCGGAGGAGCGGGCAGGAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaaacatcttggctcttacatgggttccgcccattctgagcactggctactcatttcggttaagggtttagggtttaaggttctatttttgtg---------
 ||||||||||||||| | |||  | | |||||||| ||||| ||||| ||| |||||||||| || ||||||||||||||||| |||||| | ||  |||| |  |  ||    |||  ||  | ||     |     |   |||| | |      ||||    |||| |   | | |  |||     || || ||            
CCAGCTCAAGTTCCAGAGGAACAAGAGATCTGTTGCTGAGGAACGGGCTGGACGAAAGCTTGGTGGACTCAGGGTTCTCAACTCCTACTGGGTGAATGAGgtatacttgaa----ttgagtcg-agattataacaagatagcatgaggatt-----ttcatcctagtta-gtactgatgccttatctcgctcttgttactgaacaacag

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G034794_T03 (Zea mays), 5'ss of exon 1
GCAGCTCAAGTTCCAGCGCAACTTGCGTTCTGTTGCGGAGGAGCGGGCAGGAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaaacatcttggctcttacatgg-gttccgcccattctgagcactggc--tactcatttcggttaagggtttagggtttaaggttctatttttgtg
 ||||||||||||||| | |||  | | |||||||| |||||| |||| ||| |||||||||| || ||||||||||||||||| |||||| | ||  |||| || | ||     |||    | ||| |   |   |   ||| | | |  || |  |||| ||  |   |  || | | |    |      |          
CCAGCTCAAGTTCCAGAGGAACAAGAGGTCTGTTGCTGAGGAGAGGGCTGGACGAAAGCTTGGTGGACTCAGGGTTCTCAACTCCTACTGGGTGAATGAGgtatgcttaattgagttgagcttaacaagatatcatgagaattttcatccttgtcagtactgatgccacatctggctcttgttactggacaacag--------

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G180724_T01 (Zea mays), 5'ss of exon 3
GCAGCTCAAGTTCCAGCGCAACTTGCGTTCTGTTGCGGAGGAGCGGGCAGGAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaaacatcttggctcttacatgggttccgcccattctgagcactggctactcatttcggttaagggtttagggtttaaggttctatttttgtg------
 ||||||||||||||| | |||  | | |||||||| |||||| |||| ||| |||||||||| || ||||||||||||||||| |||||| | ||  |||| |  |  || ||||||  |  | |   | ||    | |    |         |  ||||    |||| |   | | |  |||      | ||  ||        
CCAGCTCAAGTTCCAGAGGAACAAGAGGTCTGTTGCTGAGGAGAGGGCTGGACGAAAGCTTGGTGGACTCAGGGTTCTCAACTCCTACTGGGTGAATGAGgtatacttgaa-atcttgaattgtgccgagcttataacaagatagcatgagaatt-ttcatcctagtta-gtactgatgccttatctccttgttactgaacaacag

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA05G04870.1 (Glycine max), 5'ss of exon 3
GCAGCTCAAGTTCCAGCGCAACTTGCGTTCTGTTGCGGAGGAGCGGGCAGGAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaaacatcttggctcttacatgggttccgcccattctgagcactggctactcatttcggttaagggtttagggtttaaggttctatttttgtg
 || || || || ||||||| |  | | |||||||| |||||||| || ||||| ||| | || ||||||||||||||||| || |||||| | ||  |||| ||||     ||||| ||  |       ||    ||     ||   |     | || | |  | |  |  | ||    | | | ||  | ||   |  
TCAACTGAAATTTCAGCGCAGCAAGAGGTCTGTTGCCGAGGAGCGAGCTGGAAGGAAGTTGGGTGGCCTCAGGGTTCTCAATTCATACTGGGTGAATGAGgtatgtt-----atctttgcattgttgaaagtgaaacc-----tggatatgaattgctgactg-gttggactgattctattgttatgtgttgttacag--

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|37836133|gb|BJ594141.1|BJ594141
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|162203237|gb|FC379334.1|FC379334
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|37835392|gb|BJ593404.1|BJ593404
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|67727373|gb|BJ977632.1|BJ977632
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|37832817|gb|BJ590829.1|BJ590829
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|18327613|gb|BJ159616.1|BJ159616
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|7584261|gb|AW700157.1|AW700157
EST:     GAAGAAAGCTTGGAGGCCTCATGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|7047291|gb|AW477185.1|AW477185
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|18355874|gb|BJ187933.1|BJ187933
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATT
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATT
EST: gi|67704760|gb|BJ964993.1|BJ964993
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|162203238|gb|FC379335.1|FC379335
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|162260329|gb|FC435632.1|FC435632
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|18349166|gb|BJ181215.1|BJ181215
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAN                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|37824878|gb|BJ582944.1|BJ582944
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|67719044|gb|BJ969303.1|BJ969303
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|162260330|gb|FC435633.1|FC435633
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|18345767|gb|BJ177810.1|BJ177810
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|162241256|gb|FC417823.1|FC417823
EST:     GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: GAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
EST: gi|15729102|gb|BI741139.1|BI741139
EST:     TTCTCAACTCTTACTGGATCAACCAG                         GACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA
genomic: TTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCA

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: 9 (upstream exon), 34 (downstream exon)
Score: 6

GCAGCTCAAGTTCCAGCGCAACTTGCGTTCTGTTGCGGAGGAGCGGGCAGGAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaa ... gcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCAGTTATTCGCAAGGACCCAAGGATCAACTGGATTGTGAACCCCGTCCACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCTCAAGTTCCAGCGCAACTTGCGTTCTGTTGCGGAGGAGCGGGCAGGAAGAAAGCTTGGAGGCCTCAGGGTTCTCAACTCTTACTGGATCAACCAGgtgtgttgaaacatcttggctcttacatgggttccgcccattctgagcactggctactcatttcggttaagggtttagggtttaaggttctatttttgtg

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG