Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgcgtagatttgtttggatgcacagttctattgttccagtattcgtacgttttcaatcttcagatgatttcatggtattgtatgttgctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAGCTTCCACTTACTCACCACGAGTTATATAAGCAGATTGGTATTGACCCAC

Basic information

species Physcomitrella patens
transcript PP1S243_67V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 1
ttttgcgtagatttgtttggatgcacagttctattgttccagtattcgtacgttttcaatcttcagatgatttcatggtattgtatgttgctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAGCTTCCACTTACTCACCACGAGTTATATAAGCAGATTGGTATTGACCCAC
                  | | | |   |||| |  |      | || |  |   ||    |   |  | | | |     |  |   ||| |   | ||||||||||| || |||||||| ||||||||||| ||  | || || || |||||||| || || ||||||||| |||| |||||||||||||| || ||||
------------------gtaagaatttttctttcttcttgcgactcttgagggctcgtgttcttg--ggtctaagcacttctttctttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTATACAAGCAGATTGGTATCGATCCAC

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
ttttgcgtagatttgtttggatgcacagttctattgttccagtattcgtacgttttcaatcttcagatgatttcatggtattgtatgttgctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAGCTTCCACTTACTCACCACGAGTTATATAAGCAGATTGGTATTGACCCAC
                      | |      | |  |||      | | | | |     ||||     | | | |     |  ||  ||| |   | ||||||||||| || |||||||| ||||||||||| ||  | || || || |||||||| || || ||||||||| | || |||||||||||||| || ||||
----------------------gtaagaaattttctttcttactcttgaaggctcgtgttcttg----ggtctaaacacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
















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|100396152|gb|BY972260.1|BY972260
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTA
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTA
EST: gi|100439418|gb|BY961923.1|BY961923
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|162164771|gb|FC340493.1|FC340493
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|162186125|gb|FC361329.1|FC361329
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|208362233|gb|DC939657.1|DC939657
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|208357180|gb|DC942758.1|DC942758
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAAAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|208391711|gb|DC937943.1|DC937943
EST:     CTAGCATTTCGTTGTTGACACAATCGGGGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAAGCAGTAGA
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAA-GCAGTAGA
EST: gi|100428267|gb|BY977717.1|BY977717
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAG
EST: gi|100355647|gb|BY946039.1|BY946039
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAAGCA-GAGATTAGGGAAGCAGTAGA
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAA-GCAAGAGATTAGGGAAGCAGTAGA
EST: gi|208356726|gb|DC902558.1|DC902558
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|208364561|gb|DC930951.1|DC930951
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|100441057|gb|BY980678.1|BY980678
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGGAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|100371726|gb|BY948777.1|BY948777
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
EST: gi|67712869|gb|BJ966318.1|BJ966318
EST:     CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAAC                         GATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG
genomic: CTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAG

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: 22 (upstream exon), 35 (downstream exon)
Score: 7

TCATAGGCACTCCAATGCGCTAGTCGATGTGCTGCCTCCTGAAGCCGATTCTAGCATTTCGTTGTTGACACAATCGGAGAAGCCTGATGTGTCGTATAACgtacgttctt ... ctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAGCTTCCACTTACTCACCACGAGTTATATAAGCAGATTGGTATTGACCCAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtacgttttcaatcttcagatgatttcatggtattgtatgttgctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAGCTTCCACTTACTCACCACGAGTTATATAAGCAGATTGGTATTGACCCAC
       ttttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgcgtagatttgtttggatgcacagttctattgttccagtattcgtacgttttcaatcttcagatgatttcatggtattgtatgttgctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAGCTTCCACTTACTCACCACGAGTTATATAAGCAGATTGGTATTGACCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT