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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaagtttcaaaacagtaatgtagaggtgaagtttcgaatctcctgtttgggagctagtgtctcttttagtacgataagcgcaacgtttttggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAG

Basic information

species Physcomitrella patens
transcript PP1S99_129V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
caaagtttcaaaacagtaatgtagaggtgaagtttcgaatct--cctgtttgggagctagtgtctcttttagtacgataagcgcaacgtttttggg---gcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAG
     | |||   ||  ||      | |  | |||     |     |  ||      | ||   | |  ||  |   |||   ||      | |       ||||||| |||||  ||||||||||||| ||   ||||||||| ||  | ||||| |||||||| || ||||||||||| |||||||||||||| ||||| || 
----ttgtcatgccaacaagcccctgattcattttttgtacagaattacttaaatattggt-catgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G055125_T02 (Zea mays), 3'ss of exon 4
----caaagtttcaaaacagtaatgtagaggtgaa--gtttcgaatctcctgtttgggagctagtgtctcttttagtacgataagcgcaacgtttttggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAG
     | |  |      |  ||||   | | || |   | | |    ||| ||||   |  |||      |  |   |  | || |   | |||| ||     ||||||||||||  ||||||||||||| ||   ||||||||||||  | || || |||||||| || |||||||||||||| ||||| ||||| ||||| |||
ctgttataaatcggtgcccataatcctgtgatgcatactcttgggaatccagtttat-atttagatcacatcatgacagaacaaacatgaggtttatg-----cagGTACGAGTACAGATGGGCTGATGGTGTGCAGATAAAGAAACCCATAGAGGTATCAGCACCAAAATATGTGGAGTATCTGATGGATTGGATTGAAGGCCAG

upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G098819_T02 (Zea mays), 3'ss of exon 3
caaagtttcaaaacagtaatgtagaggtgaagtttcgaatctcctgtttgggagctagtgtctcttttagtacgataa--gcgcaacgtttttggggc----gcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAG
      |     | |     ||     | |   |  ||  |   | ||||| |  |||| | | |||   |   || |   |  |||  |  || ||     ||||||| |||||  ||||||||||||| ||   ||||||||||||  | || || |||||||| || ||| |||||||||| ||||| ||||| ||||| |||
------tctgttataaattggtgcccataatcctgtgatgcatatttttggaaattagtttatatttagatcatatcatgacagaacaatcatgaggtttatgcagGTATGAGTACAGATGGGCTGATGGTGTGCAGATAAAGAAACCCATAGAGGTATCAGCACCAAAATATATGGAGTATCTGATGGATTGGATTGAAGGCCAG

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|162170893|gb|FC346584.1|FC346584
EST:     CCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: CCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|37841636|gb|BJ599644.1|BJ599644
EST:     ATGTCCGCAGGACCCAA                         GTACGAGGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAG
genomic: ATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGA-GTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAG
EST: gi|162246776|gb|FC423874.1|FC423874
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162230785|gb|FC406416.1|FC406416
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162240619|gb|FC419162.1|FC419162
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|67575885|gb|BJ948709.1|BJ948709
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162215256|gb|FC391648.1|FC391648
EST:     ATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162170894|gb|FC346585.1|FC346585
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162266887|gb|FC443001.1|FC443001
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|67726815|gb|BJ977074.1|BJ977074
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|67570910|gb|BJ943734.1|BJ943734
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTTACGAGTATNGATGGGCTGATGGGGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGT-ACGAGTATCGATGGGCTGATGGGGT
EST: gi|37844367|gb|BJ602375.1|BJ602375
EST:     GCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: GCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162230786|gb|FC406417.1|FC406417
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162240620|gb|FC419163.1|FC419163
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|67694230|gb|BJ954463.1|BJ954463
EST:     TGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: TGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162215557|gb|FC391649.1|FC391649
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|7207622|gb|AW561562.1|AW561562
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|67694212|gb|BJ954445.1|BJ954445
EST:     CCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: CCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|18364712|gb|BJ196785.1|BJ196785
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162266886|gb|FC443000.1|FC443000
EST:     ACCGAGTTCTGCACACCTGAGAACTGTCNTACTATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
EST: gi|162246775|gb|FC423873.1|FC423873
EST:     ATGTCCGCAGGACCCAA                         GTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT
genomic: ATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGT

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: 30 (upstream exon), 33 (downstream exon)
Score: 24

CCGTGGATTTTTTCAACCAGGTGAATCTACTCTATGGAACATTGACCGAGTTCTGCACACCTGAGAACTGTCCTACTATGTCCGCAGGACCCAAgtactactct ... tggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgggagctagtgtctcttttagtacgataagcgcaacgtttttggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAG
                                       cgttttt  CT-rich tract
                   ttttagta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaagtttcaaaacagtaatgtagaggtgaagtttcgaatctcctgtttgggagctagtgtctcttttagtacgataagcgcaacgtttttggggcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG