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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggacgtggaggtgactgcgggcgtggattgggttggttggttggttggattggggtgggagctgcattggggatttttgacggttggtgtgtggttgggtgggggattgacgcgattgatgattgcgggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGGCGGAGCTTCGAGGACATGTGCGCGCAGATGTACTACAGGGGGAAGATGT

Basic information

species Physcomitrella patens
transcript PP1S199_145V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S199_145V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g02900.1 (Oryza sativa), 3'ss of exon 1
gtgagtggacgtggaggtgactgcgggcgtggattgggttggttggttggttggattggggtgggagctgcattggggatttttgacggttggtgtgtggttgggtgggggattgacgcgattgatg--attgcgggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGGCGGAGCTTCGAGGACATGTGCGCGCAGATGTACTACAGGGGGAAGATGT
                                 |||   | |    |  | ||  | |    || |    |||         ||| | | || |    |  |   | |  |  |  |  |||| ||    || |    |   |||   || |||   || || |   ||||||||||||||||||||||  | || || |  |||||||| ||||||||||| ||||||||| | || |||||||
---------------------------------ttg---tagccactgtggtgcttcgatagggaaaactcatc--------ttgtctgctgttacaagtgttaatagtagcctt-cttgattcatatcgtttcattttccacagGCTGTCACGCGGGAAGAGGCTTTGGAGCTGTACGAGGACATGGTTCTTGGCCGTATTTTCGAGGATATGTGCGCGCAAATGTACTACCGTGGCAAGATGT

upper sequence: PP1S199_145V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv15s0048g02580.t01 (Vitis vinifera), 3'ss of exon 1
gtgagtggacgtggaggtgactgcgggcgtggattgggttggttggttggttggattggggtgggagctgcattggggatttttgacggttggtgtgtggttgggtgggggattgacgcgattgatgattgcgggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGGCGGAGCTTCGAGGACATGTGCGCGCAGATGTACTACAGGGGGAAGATGT
                                         |    |||   | |||| |      | | | ||     || || ||  ||  |   |         | | ||   |     || |  ||  |    |  ||| || | ||||  || |||||| |||||||||| || |||||||| |||||  |    || ||||||||||| || ||||||||||||||||| || ||||
-----------------------------------------gagaattgcgagaattgtgcaaatggtttcgtttacttttctt-acattttctcaattaccaaacagagcataatctttcgtg-tctttttgtctgtttcagCTGATTACGAGGGAGGAAGGGTTGGAGCTGTATGAAGACATGGTATTGGGTAGAGCTTTTGAGGACATGTGTGCTCAGATGTACTACAGGGGCAAAATGT

upper sequence: PP1S199_145V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ25051 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtggacgtggaggtgactgcgggcgtggattgggttggttggttggttggattggggtgggagctgcattggggatttt-tgacggttggtgtgtggttgggtgggggattgacgcgattgatgattgcgggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGGCGGAGCTTCGAGGACATGTGCGCGCAGATGTACTACAGGGGGAAGATGT
                            |||  |         |  ||  |    ||    | |     |   |||  ||      | |  ||| |   || |   |||     |||||  |||   | |||     |   ||| | |||||||  || || ||  ||||||| |||||||||||| |  | |||||  |||||||||| ||||| || |||||||||||| |    |||||||
----------------------------gtgagtccctccctctattt--tcaccttattctcgacatagatctggccatgcagcaatgcatggcgatcggcta--tggattcctgacgaaattctcgcttgtc---tccccagCTCGTGACGAGGGAAGAGGGATTGGAGCTCTACGAGGACATGATCCTCGGGCGCTGCTTCGAGGATATGTGTGCCCAGATGTACTACCGCTCCAAGATGT

upper sequence: PP1S199_145V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ29991 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtggacgtggaggtgactgcgggcgtggattgggttggttggttggttggattggggtgggagctgcattggggatttttgacggttggtgtgtggttgggtgggggat--tgacgcgattgatgattgcgggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGGCGGAGCTTCGAGGACATGTGCGCGCAGATGTACTACAGGGGGAAGATGT
                                                                         |  ||   |    |  |   || | | | || |  ||  |  |||||  |||   |  ||     |   ||| | |||||||  || || ||  ||||||| |||||||||||| |  | |||||  |||||||||| |||||||| |||||||||||| |    |||||  
------------------------------------------------------------------------atctggccatgcagcaatgcatg-gcgatcggctatggattcctgacgaaattctcgcctgtc---tccccAGCTCGTGACGAGGGAGGAGGGATTGGAGCTCTACGAGGACATGATCCTCGGGCGCTGCTTCGAGGATATGTGCGCCCAGATGTACTACCGCTCCAAGAT--

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|208369639|gb|DC932579.1|DC932579
EST:     CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
EST: gi|100436937|gb|BY979601.1|BY979601
EST:     CGGTGACGGAGAAGCCAAATAGCGGGGCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGGAGCTGTACGAG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGG-AGCTGTACGAG
EST: gi|100417020|gb|BY993204.1|BY993204
EST:     CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
EST: gi|208388684|gb|DC941511.1|DC941511
EST:     CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
EST: gi|18368641|gb|BJ200726.1|BJ200726
EST:     CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
EST: gi|18328910|gb|BJ160916.1|BJ160916
EST:     CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
EST: gi|100442192|gb|BY963085.1|BY963085
EST:     CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
EST: gi|208393620|gb|DC904336.1|DC904336
EST:     CGGTGACGGANAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
EST: gi|100425849|gb|BY977151.1|BY977151
EST:     CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
EST: gi|100403173|gb|BY991071.1|BY991071
EST:     CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTG                         TTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG
genomic: CGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGG

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

TCGAGTTGCAGGCGGCGGCAATGTGCGGGCTGCTGTGTCCGCGTCGAAGGCGGTGACGGAGAAGCCAAATAGCGGGTCGAAGTCGGACAAGGCAGATTTGgtgagtggac ... ggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGGCGGAGCTTCGAGGACATGTGCGCGCAGATGTACTACAGGGGGAAGATGT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtggacgtggaggtgactgcgggcgtggattgggttggttggttggttggattggggtgggagctgcattggggatttttgacggttggtgtgtggttgggtgggggattgacgcgattgatgattgcgggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGGCGGAGCTTCGAGGACATGTGCGCGCAGATGTACTACAGGGGGAAGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG