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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgtctctgcaaggccttttccaacctcaattcacaatcttattcgctgcttagtcttttctgggagtttaatgctatatttactttgcctagtctatgtctactgttggtttctattgaattcacattctatgatccggcactgaccttgctgacgcgttatgtttgacaacctttttgtctacgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCTGGAGGAGTTCACCTCGAAATGACAGGACAGAATGTGACTGAATGTGTGG

Basic information

species Physcomitrella patens
transcript PP1S36_31V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S36_31V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G10670.1 (Glycine max), 3'ss of exon 4
gtgagcgtctctgcaaggccttttccaacctcaattcacaatcttattcgctgcttagtcttttctgggagtttaatgctatatttactttgcctagtctatgtctactgttggtttctattgaattcacattctatgatccg-gcactgaccttgctgacgcgttatgtttgacaacctttttgtctacgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCTGGAGGAGTTCACCTCGAAATGACAGGACAGAATGTGACTGAATGTGTGG
                                                                                             | |    || |  |||||     |  ||  | || | |||  || ||    ||    |  ||  ||| || |    |||    |  |||    |||  |||  ||||| || || ||  | |||||||||||||||||||| ||||| |  ||| | || || ||||| || || |||||||| |||||||||||||| ||  | |
-------------------------------------------------------------------------------------------agcaacatcatatg-actgtcaaccttgat--agttgatatttgattattgatgcctctaatttattgatgcctctaattt----atatttcccccta-atgggacagGAGGAGGTGAAATCATTCTTCGACGTGCATGAACAAGAAGGAAGCCACCCAGGTGGGGTTCATCTAGAGATGACAGGTCAGAATGTGACTGAGTGCATTG

upper sequence: PP1S36_31V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagcgtctctgcaaggccttttccaacctcaattcacaatcttattcgctgcttagtcttttctgggagtttaatgctatatttactttgcctagtctatgtctactgttggtttctattgaattcacattcta-tgatccggcactgaccttgctgacgcgttatgtttgacaacct---ttttgtctacgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCTGGAGGAGTTCACCTCGAAATGACAGGACAGAATGTGACTGAATGTGTGG
                                                                                                      |  |         |  | ||| |||   || |||   |  |   |  |    |  |   |  ||||     |  | ||    ||  |  |     |  |||  ||||| |  ||||||||||||||||| || || |||||||  ||| | |||||| ||||||| |||||||| || ||||| ||||| || ||  | |
------------------------------------------------------------------------------------------------------gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattattgcaaatcatctaatgttaattgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
















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|162168088|gb|FC343778.1|FC343778
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|208374364|gb|DC948396.1|DC948396
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|67695342|gb|BJ955575.1|BJ955575
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162156274|gb|FC332298.1|FC332298
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|18341413|gb|BJ173448.1|BJ173448
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162174782|gb|FC352198.1|FC352198
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162176950|gb|FC353627.1|FC353627
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|18336945|gb|BJ168968.1|BJ168968
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|67691461|gb|BJ951694.1|BJ951694
EST:     ACTCGCCCGNTNGACTCCATTTTG                         GACGAAGTTAAGGCTTTNTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: ACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162185169|gb|FC362303.1|FC362303
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|37827918|gb|BJ585930.1|BJ585930
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACA--AAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162156273|gb|FC332297.1|FC332297
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162219668|gb|FC395664.1|FC395664
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162167805|gb|FC344535.1|FC344535
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162168089|gb|FC343779.1|FC343779
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162219667|gb|FC395663.1|FC395663
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162185170|gb|FC362304.1|FC362304
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162248091|gb|FC420096.1|FC420096
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162151760|gb|FC328617.1|FC328617
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162168852|gb|FC345050.1|FC345050
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162194172|gb|FC369684.1|FC369684
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162162347|gb|FC338311.1|FC338311
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162199199|gb|FC374619.1|FC374619
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTTTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162187913|gb|FC364487.1|FC364487
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162168851|gb|FC345049.1|FC345049
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|67691441|gb|BJ951674.1|BJ951674
EST:     CTCGCCCGTTTGACTCCA-TTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162174783|gb|FC352199.1|FC352199
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|67720594|gb|BJ970853.1|BJ970853
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162176951|gb|FC353628.1|FC353628
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACA
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACA
EST: gi|162163355|gb|FC339681.1|FC339681
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|67725671|gb|BJ975930.1|BJ975930
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
EST: gi|162270227|gb|FC447239.1|FC447239
EST:     CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTG                         GACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT
genomic: CTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCT

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: 29

CCAGGCAGGCATTATTGTCACATGGGTGTGTGACCCGATGCATGGAAACACTATTAAGGCGCCCTCGGGAATCAAAACTCGCCCGTTTGACTCCATTTTGgtgagcgtct ... cgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCTGGAGGAGTTCACCTCGAAATGACAGGACAGAATGTGACTGAATGTGTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcactgaccttgctgacgcgttatgtttgacaacctttttgtctacgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCTGGAGGAGTTCACCTCGAAATGACAGGACAGAATGTGACTGAATGTGTGG
                    ttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgtctctgcaaggccttttccaacctcaattcacaatcttattcgctgcttagtcttttctgggagtttaatgctatatttactttgcctagtctatgtctactgttggtttctattgaattcacattctatgatccggcactgaccttgctgacgcgttatgtttgacaacctttttgtctacgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCTGGAGGAGTTCACCTCGAAATGACAGGACAGAATGTGACTGAATGTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG