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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatcaacctagcggttatttcattcacacaatctcccatttactttcattgaatatttatgaagtttcaagcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcag

Basic information

species Physcomitrella patens
transcript PP1S285_10V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S285_10V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G166281_T01 (Zea mays), 5'ss of exon 2
TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatcaacctagcggttatttcat----tcacacaatctcccat--ttactttcattgaatatttatgaagtttcaagcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcag
 |||||||||||||| ||||| || ||||| ||||| || || ||||| ||||||||||| |||||||||| ||  || || ||||| ||||     || |||  | |          ||| || | |    |  || |  |   ||   | | ||| | | | |  | ||   || |   |  |  |||  || | |                                     
GATGGACTATGCATTTGAGTTCATCATCAACAATGGCGGAATCGACACCGAGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttgcttccatagtttttccttgattttccaaagaccagcagcgtcatttttacttactgctgatcttgtgtgttgggtccatc-tattgcag------------------------------------

upper sequence: PP1S285_10V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA04G04400.1 (Glycine max), 5'ss of exon 2
TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatcaacctag--cggttatttcattcacacaatctcccatttactttcattgaatatttatga-agtttcaagcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcag
| |||||||||| || ||||| |||||||| |||||||| |||||||||||  ||||||| || |   | |     ||||||   || ||| |    |  || ||| | | | | |     ||  |  |||   | |  || | | |  |||   |  |||| |||| | || ||     |||  ||  ||| ||  |                                  
TGTGGACTATGCCTTTGAGTTCATTATCAACAATGGTGGCATTGACACTGAAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagttttacctttgattctttgataaattagtaaatgcttctaatagcttcattctaatacttataatagattt---tattcttcttatc-tatag----------------------------------

upper sequence: PP1S285_10V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA14G09440.1 (Glycine max), 5'ss of exon 2
TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatcaacctagcggttatttcattcacacaatctcccatttactttcattgaatatttatgaagtttcaagcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcag
||||||||||||||| ||||| |||||||| ||||| || |||||  ||||  ||||||| ||||||   |     |||||| | || ||       || || |||| |    |   | |||||| ||    ||||||      |||       |   |||   | || ||   |   ||| |   || ||  ||| |  || | |  |  |                 
TATGGACTATGCATTTGAGTTCATTATCAACAATGGCGGCATTGATTCTGAAGAGGATTACCCTTACCGTGGTGTTGATGGTAGATGTGACACATATAGGgttagtaacttggtcctgattatttgatg---acaatcaat-gcttataaaagatatttatcactcaaattcttattgttttttctat-gtttggttattttgcttttgcgcag---------------

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|162186545|gb|FC363309.1|FC363309
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|162157752|gb|FC335466.1|FC335466
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|162255174|gb|FC431484.1|FC431484
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|162177962|gb|FC354068.1|FC354068
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|100397513|gb|BY990264.1|BY990264
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         GGGAATTCCAA-GTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|100433239|gb|BY978858.1|BY978858
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|162163721|gb|FC340307.1|FC340307
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA

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: 66

TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAATCTGAGAGCGCTCTGATGAAGGCACTGACGAAAAACCCTGTCAGTGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatcaacctagcggttatttcattcacacaatctcccatttactttcattgaatatttatgaagtttcaagcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA