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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtttgtgttctttttgtaacgagcttgacattattttcctttcatattttggggttgagtctgattggtttcgttttgtttggggcctaaataattttagttcgtgcgcactgaattgtggcacgttctttgaattgatatgaggaacgcctgtgtag

Basic information

species Physcomitrella patens
transcript PP1S249_49V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S249_49V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G134613_T01 (Zea mays), 5'ss of exon 3
AAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtttgt--gttctttttgtaacgagcttgacattattttcctttcatattttggggttgagtctgattggtttcgttttgtttggggcctaaataattttagttcgtgcgcactgaattgtggcacgttctttgaattgatatgaggaacgcctgtgtag
                                               || ||||| ||||| ||||| | |||||||||| ||||||| |||||||||||||  |   |||      | | | | ||  |   |||  ||| || ||  |   | |||| ||      |   |||  ||  ||  | | |      |   | ||                                                               
-----------------------------------------------GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatttcacgagtatctctttagtgcatttg-tatt-ttctctatcagtttttttggac---attatattttttctgtact-tctaaaagttgccttatac-------------------------------------------------------------

upper sequence: PP1S249_49V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G014975_T01 (Zea mays), 5'ss of exon 2
AAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtttgtgttctttttgtaacgagcttgacattattttcctttcatattttggggttgagtctgattggtttcgttttgtttggggcctaaataattttagttcgtgcgcactgaattgtggcacgttctttgaattgatatgaggaacgcctgtgtag
                                               || ||||| ||||| ||||| | |||||||||| ||||||| |||||||||||||    ||||      | |||    |  |  |  |  ||   || |||   | || |||  ||   |   ||||   |  ||||   ||        | | |  |                                                            
-----------------------------------------------GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATCGACAAGAAAAAgt---cagttccgaaccatttcaagattatttcaa--ttgcatttcttgacttttatggtttttcctgacattgcaatttttttccctgtacttctgaaagtagt------------------------------------------------------------
















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|162238575|gb|FC418964.1|FC418964
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|18365712|gb|BJ197789.1|BJ197789
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162269518|gb|FC445074.1|FC445074
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|37826926|gb|BJ584938.1|BJ584938
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162263756|gb|FC438921.1|FC438921
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATTTCAGACATAGCCAAGAAAAA                         GTCCCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTTTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|22491699|gb|BU051622.1|BU051622
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162265957|gb|FC442960.1|FC442960
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACTTTTCAGACATAGCCAAGAAAAA                         GTCCCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTTTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|208372756|gb|DC952643.1|DC952643
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162201747|gb|FC377499.1|FC377499
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|18353808|gb|BJ185863.1|BJ185863
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|18325320|gb|BJ157316.1|BJ157316
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|22132370|gb|BQ827117.1|BQ827117
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162243663|gb|FC420679.1|FC420679
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|37835281|gb|BJ593293.1|BJ593293
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162260417|gb|FC435043.1|FC435043
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|37845489|gb|BJ603497.1|BJ603497
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|67570411|gb|BJ943235.1|BJ943235
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|67693686|gb|BJ953919.1|BJ953919
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162226589|gb|FC402491.1|FC402491
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162244437|gb|FC422610.1|FC422610
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162260403|gb|FC435042.1|FC435042
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|67570144|gb|BJ942968.1|BJ942968
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162237156|gb|FC413523.1|FC413523
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162238574|gb|FC418963.1|FC418963
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|208375486|gb|DC937001.1|DC937001
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|7583876|gb|AW699778.1|AW699778
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|208392197|gb|DC957276.1|DC957276
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162237157|gb|FC413524.1|FC413524
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162244436|gb|FC422609.1|FC422609
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|18347837|gb|BJ179884.1|BJ179884
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|22492458|gb|BU052381.1|BU052381
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|162263757|gb|FC438922.1|FC438922
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
EST: gi|37823882|gb|BJ581948.1|BJ581948
EST:     ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAA                         GTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG
genomic: ATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAG

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: 195

AAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtt ... gcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAGAAAGCGCATCAAGTTAAGTTCTGAGAAGGCCATCTTCATTTTCGTGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtttgtgttctttttgtaacgagcttgacattattttcctttcatattttggggttgagtctgattggtttcgttttgtttggggcctaaataattttagttcgtgcgcactgaattgtggcacgttctttgaattgatatgaggaacgcctgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA