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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgttcggtgttggagcagggggattgcatcacgcagggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctggaatgaggg...

Basic information

species Physcomitrella patens
transcript PP1S383_1V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os02g05330.1 (Oryza sativa), 5'ss of exon 4
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgta---ttccgttcggtgt-tggagcagggggattgcatcacgcag---ggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctggaatgaggg
||  |||||| | ||  || |  | || ||| | |||  ||| |||   |||||||||||||| || ||||||||||| || || || || |||||||||||    ||| |  | |    |    | |    | | | ||   |||   | ||||  |   ||  |   | | |   | |||||  ||  |  || ||   | |   
GTTTGACATGCTACGTCGGCAATCTCTCCGCCCAGACCACATTAAGATGTTTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttctgaccagcccattattctgctataatacctccaacagtttgtatggctgatcttttacattatgt---cttctgtagtgttcatgtttgtg-taa---

upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgttcggtg-ttggagcagggggattgcatcacgcagggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctg-gaatgaggg
||  || ||| |||||||  |  |||| |   | ||   |||||||   |||||  |||||||||| ||||| |||||||| || || ||||||||||||||| |     |  |  ||    |       ||   |         |   |        |    ||| |  |  | | |||| |     | ||  || |   |
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgtttttt-acaagtaatacctacacttgtctacggattt-ttttaaattgatgtgtaaacgttcg

upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA04G05580.1 (Glycine max), 5'ss of exon 4
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccg----ttcggtgttggagcagggggattgcatcacgcagggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctggaatgaggg-
 |  |||||| |||||||| |  || ||||| | ||   ||||| |   |||||  |||||||||| ||||||||||| ||||| || || |||||||||||  ||      | |  |||||           |||| |||  |     |  |     ||  | |  | || ||     | ||  |   | | |  | ||     
ATTTGACATGCTGCGCAGGCAATCATTGCGCTCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcattttcccatgttgctctcttttatttgcttcattctattgtttgttgtgttggaatacgattttg-----gcttaaaaataatatttagtgttttt

upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA06G05580.1 (Glycine max), 5'ss of exon 4
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgttcggtgttggagcagggggattgcatcacgcagggatgggcgtctttcaagtctg--tttgtgcctctgttttgagccagtctggaatgaggg
 |  |||||| || ||||  |  |  ||||| | ||   ||||| |   |||||  |||||||||| ||||||||||| ||||| || || |||||||||||  ||   |   |      || |     ||  ||               || | |  | | ||  ||       || ||| |        | ||||     
ATTTGACATGCTGTGCAGACAATCTTTGCGCCCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcatt--ttcctatgctgctctcttttattggcttcattctattgtttgtggattttggcttaaaaatactatttagttttttatttgaattttca

upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G00950.1 (Glycine max), 5'ss of exon 4
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgttcggtgttggagcagggggattgcatcacgcagggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctggaatgaggg---
||  |||||| |||| ||| |  | || ||| | || | ||| |||   |||||  |||||||||| ||||| |||||||| || || |||||||||||||| |    ||  |  ||           ||    |   |||   ||      |||    ||||||      ||   |    | ||  |||   |||  ||   
GTTTGACATGCTGCGGAGGCAGTCTCTTCGCCCAGATTGCATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttattttg-attaccatgttttcat-atttagtgcactaatttat-ccttggttgtctgtcctatacttgttgactatcctatctcttatgttggtaa

upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv04s0008g00980.t01 (Vitis vinifera), 5'ss of exon 1
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgttcggtgttggagcagggggattgcatcacgcagggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctggaatgaggg
      || | || |  ||  | | || |  || ||||||||||||   ||||| ||||||||||| ||||| ||||| ||| | || |||||||||||||| ||    | | | |||       | | || |||     | | ||    ||     ||   |||  || |||   || |   |  | ||| |       
------CACGCTGAGGCGGGGCTCTCTCCATGCTGACTCCATCAAGATGTTTGTTCTGGATGAGGCTGATGAAATGCTCTCTAGAGGCTTTAAGGATCAGgtctttatctagctcttgtcc----gtgttttcat-----aagaatttttgtagccaaaacttgt--gttcctaaattgttttcttgcctgcag------

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|100415489|gb|BY992868.1|BY992868
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|100387935|gb|BY970680.1|BY970680
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162186231|gb|FC362163.1|FC362163
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162195203|gb|FC371426.1|FC371426
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|100396855|gb|BY953861.1|BY953861
EST:     TGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGGTTTA-GGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCGAGTGGGTGTTTTC
genomic: TGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGG-TTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162211807|gb|FC387471.1|FC387471
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162263015|gb|FC439330.1|FC439330
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|208348012|gb|DC905335.1|DC905335
EST:     TTGTGCTGGATGANGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCC-AGAN-CTTCAAGTGGGTGTTT-C
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162155800|gb|FC331829.1|FC331829
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162267873|gb|FC444474.1|FC444474
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162189204|gb|FC366726.1|FC366726
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|100445358|gb|BY982987.1|BY982987
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162180442|gb|FC355863.1|FC355863
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|208362032|gb|DC950481.1|DC950481
EST:     TGTGCTGGATGAGGCCGATGAGATGCTTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TGTGCTGGATGAGGCCGATGAGATGC-TTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162189433|gb|FC365447.1|FC365447
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162163659|gb|FC339764.1|FC339764
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
EST: gi|162162744|gb|FC337798.1|FC337798
EST:     TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAG                         ATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC
genomic: TTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTC

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: 34 (upstream exon), 34 (downstream exon)
Score: 52

GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgtt ... atacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTCTCTGCTACCATGCCTCCTGAAGCCCTCGAGATCACAAGGAAGTTCATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgttcggtgttggagcagggggattgcatcacgcagggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctggaatgaggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG