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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgagtgatgctttctaaaattgtaagctagaggcattactctgtttgatcgagtttctaaattttcttttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA

Basic information

species Physcomitrella patens
transcript PP1S10_319V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 2
gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgagtgatgctttcta----aaattgtaagctagaggcattactctgtttgatcgagtttctaaattttcttttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA---------
                                       ||| | | | || ||| |  || ||  ||||| ||    ||| || |   | ||| |   |||   ||   || |    | | | | || ||| |  |||| |  ||||         |  ||||||  || |||||||| ||| ||||||| ||||||||||||||||||   ||||||||||||||| |  | || |          
------------------------------------tttagcttttttcca-aatgatcgattgtagctttttagttcaaactgcag--tggagcctgaactgacttgtttctaaacacaatactctcctttttaccagGAGGTGATG---------CAAGTGGAAGATCTAAGCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCG

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 2
gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgag-tgatgctttctaaaattgtaagctagaggcattactctgtttgatcgagtttctaaatt-ttcttttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA---------
                                            |||| |    | | |  | ||    ||| ||    ||  |  |  |   |||||      ||| | ||| | |   |  || |  |||| |  |  |||| ||    | |||  |||| ||||| ||||| ||| |  |||||||||| ||| | ||||||||||  |||||||||||||||||| | || |          
------------------------------------------tcctgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaacaattacaacacctga-caagtatttgtctcattttcatctttcgcgacaagAAGG---GGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCG

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgagtgatgctttctaaaattgtaagctagaggcattactctgtttgatcgagtttctaaatt-ttcttttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA------------
                                           |  | |  ||||| |    ||    ||| ||    ||  |  |  |   |||||      ||| | ||| | |   |  || |  |||| |  |  |||| ||    | |||  |||| ||||| ||||| ||| |  |||||||||| ||| | ||||||||||  |||||||||||||||||| | || |             
-----------------------------------------tgtgcgctttgaatttgc---tgtctgtttttatctctggtatgtgaaacaattacaacacctga-caagtatttgtctcattttcatctttcgcgacaagaagG---GGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgagtgatgct--ttctaaaattgtaagctagaggcattactctgtttgatcgagtttctaaattttcttttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA------
                               |   |    | | ||||   |  |  | ||| |||||    | ||   | ||  ||     |   | ||     ||  ||  | | | |       ||   ||||| ||| || |||   || || ||  |      ||||||||||||  | |||||||| ||| | ||||||||||| ||||| |||||||||||||| || |       
-----------------------------gctcagcgtctggcgctgtc--ggctgggcgagcgatgccagctttagtttcgtcggcccacagggatgctgaacatgg-cgcatgtgtga-----tgttggctgcagATGAGGAGGGT---GGCGCTGGCCGCGG---CAAGCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGAC

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgagtgatgctttctaaaattgtaagctagaggcattactctgtttgatcgagtttctaaattttct---tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA--------------
                                                                                                              ||| |||  || | |   |||||| |||| || |||||  | ||          || || ||||| |||||  | |||||||| ||| ||||||| ||||| ||||| || |||||||||||||| |               
--------------------------------------------------------------------------------------------------------------gttcctactttctttatgtttcttccaggcgagGATGGAACGGG---------GAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA

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|162210245|gb|FC386730.1|FC386730
EST:     GGATGAGGATGATGTCCTTGATGGAGCTGACGGCCAAGGTGAAG                         GTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: GGATGAGGATGATGTCCTTGATGGAGCTGACGGCCAAGGTGAAGgtctgttgtc ... tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|37847320|gb|BJ605328.1|BJ605328
EST:     AGCTGACGGCCCAAGGTGAAG                         GTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: AGCTGACGG-CCAAGGTGAAGgtctgttgtc ... tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|67694196|gb|BJ954429.1|BJ954429
EST:     GACGAGGATGAGGATGATGTCCTTGATGGAGCTGACGGCCAAGGTGAAG                         GTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: GACGAGGATGAGGATGATGTCCTTGATGGAGCTGACGGCCAAGGTGAAGgtctgttgtc ... tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|67570895|gb|BJ943719.1|BJ943719
EST:     TGATGTCCTTGATGGAGCTGACGGCCAAGGTGAAG                         GTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: TGATGTCCTTGATGGAGCTGACGGCCAAGGTGAAGgtctgttgtc ... tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|162200867|gb|FC377062.1|FC377062
EST:     GCCAAGGTGAAG                         GTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: GCCAAGGTGAAGgtctgttgtc ... tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|37840258|gb|BJ598266.1|BJ598266
EST:     GCCAAGGTGAAG                         GTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: GCCAAGGTGAAGgtctgttgtc ... tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|7067581|gb|AW497436.1|AW497436
EST:     CCAAGGTGAAG                         GTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: CCAAGGTGAAGgtctgttgtc ... tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGA

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: 112

GATGAGCCCACTATTGAGGACGCGAAGGACGATGATGATGACGACGACGACGACGAGGATGAGGATGATGTCCTTGATGGAGCTGACGGCCAAGGTGAAGgtctgttgtc ... tttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagctagaggcattactctgtttgatcgagtttctaaattttcttttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA
                                ttctaaa  putative branch site (score: 112)
                                       ttttcttttcttgc  CT-rich tract
                               tttctaaattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttgtcaacgacccttgccaacgtctattgacccaagcctctgttcagaattagtgagtgatgctttctaaaattgtaagctagaggcattactctgtttgatcgagtttctaaattttcttttcttgcagGTGAAGATGGTTCAGGTGCGGGTGGAAAGTCCAAGCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC