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

gtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtatactcacgtagtctgtacatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG

Basic information

species Physcomitrella patens
transcript PP1S139_2V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os09g31970.1 (Oryza sativa), 3'ss of exon 2
gtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgttta-gctgtacagtatactca-cgta-gtctgtacatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG
         |  ||    |  |  || | ||    ||    |  ||||   |  |      ||| || | ||| || | | | || | | ||  ||   | |    |||||||||||||| | ||||| ||  || | |||||||| |||||||| || |||||||||||||| |||||||||||| |  | |||| ||| || ||   
---------acaactgtatcttgtgtacatcacaacataatagcttttaaatctttccatactttttcatgctttataatttcctaaacttatatcctcatacaaacagGTAACTTCTGTTCTGACAAAAAGTCAGCTGCTGTAAATTGGATTGAGGGACGTGGAAAGTCTGTGGTTTGTGAGGCAGTAATCAAAGAGGAAGTTGTGAA

upper sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g48330.1 (Oryza sativa), 3'ss of exon 3
gtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtatactcacgtagtctgtacatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG
 |||   | |  |    | ||||    ||   | |   |||||   ||| |          ||||| |     | ||   |  | |  || |||||     | |||||||||  ||  | |||||||| || ||||||||||||||||| || || || || || ||||| ||||||||||| ||| | ||||| || || || | 
-tttttgaaacaat--gggtgttcacactatctgtt--ttcatcaattcaccatgtattttcttgtctttgcatgcacattgatgaattaatctgtgtgcat-cagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGTGCA

upper sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G058095_T02 (Zea mays), 3'ss of exon 1
gtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtatactcacgtagtctgtacatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG
 ||||       | |   || || |  |        |  | || | ||| | ||| |      ||  | |   | |  || | | |  |||||| ||       ||||||||||||| | ||||||||  || | ||||| |||||||||||||| ||||| ||||| || |||||||||||| |  | || |  || || ||   
ttttgtggtggaatct--ttattagaacccgaa---aaatgatctcttcccatgtatctttgatgccttgtgtttcctta-agtaatatagtctttatcaaaatagGTAACTTCTGTTCTGACAAGAAGTCAGCTGCTGTGAACTGGATTGATGGCCGTGGGAAGTCGGTGGTTTGTGAGGCAGTAATCAAGGAAGAAGTTGTGAA

upper sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G001645_T01 (Zea mays), 3'ss of exon 2
gtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtat--actcacgtagtctgtacatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG
                  | | ||    ||  ||  | | ||     | | || |       ||| |    ||||   | |  ||| |  || ||||||       ||||||||||||| | ||||||||  || | ||||| |||||||| ||||| ||||| ||||| || ||||| |||||  |  | || |  || || ||   
--------tgcagttttttgggtgagattttattagaatccacaaaattgtttcttgccattttgatgccttgtattttcttaactaatatattctgtaacaaaatagGTAACTTCTGTTCTGACAAGAAGTCAGCTGCTGTGAACTGGATCGATGGCCGTGGGAAGTCGGTGGTTTGCGAGGCGGTAATCAAGGAAGAAGTTGTGAA

upper sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G136465_T01 (Zea mays), 3'ss of exon 3
gtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtatactcacgt-agtctgtacatgtgc-agGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG
   |   |||||   ||  | | | |       ||  | ||  || || || |  ||    | |    ||   |      || ||||||    || |   | | | ||||||||  ||| | ||||||||  |  |||||||||||||||| || ||||| || || ||||| ||||||||||| |   | |||||||  || || | 
ccatttgacatggaacaaat-tcgttgtaataattatgatctgttattagcattcctc---cctccccagtcatg----gtattcacgttgacctttttttataccagGTAACTATTGTTCAGACAAGAAGGCTGCAGCTGTAAACTGGATAGAAGGTCGCGGGAAATCTGTTGTTTGTGAGGCCACAGTCAAAGGGGGAGTTGTGCA

upper sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G135085_T01 (Zea mays), 3'ss of exon 2
gtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgc--ttgtctagcgcttgtttagctgtaca-gtatactcacgtagtctgtacatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG
        ||      |   |||  |  |           || |  |  ||  |  ||   | |  |    | | | || ||  |||  | |  | | || |||  |||||||||  ||| | ||||||||  |  |||| ||||||||||| || |||||||| || ||||| ||||||||||| |   | |||||||  || || | 
--------cagttattaagcgttattgttcaaaaaagaaacaatcatcagcattcctccctccccagccatggtatgcacgttgactttctttttatatatatgc-cagGTAACTATTGTTCAGACAAGAAGGCTGCAGCCGTAAACTGGATAGAAGGTCGTGGGAAATCTGTTGTTTGTGAGGCCAGAGTCAAAGGGGGAGTTGTGCA

upper sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv18s0122g00610.t01 (Vitis vinifera), 3'ss of exon 2
gtttgca--acatgaccca-gttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtatactcacgtagtctgtacatgtgc-agGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG
 || | |  |||  |   | ||| |||    |    | | ||  | |  |||   ||| |   || | | | | | |   ||| |        ||||    ||| || ||| || || ||| | |||||||||||| | ||||||||||||||||| || ||||| |||||||| |||||||||||| |  | || | ||| || ||| |
attagtagaacagcatttatgttcttgacattgttatactgtctactagttc---tgtttgatgcctctattgatttgtcgtacat-------gtctccctatgcgccagGAAATTTTTGTTCAGACAAGAAACCAGCTGCTGTAAACTGGATTGAAGGGCGTGGTAAGTCTGTGGTTTGTGAGGCAGTCATCAAGGAGGATGTGGTAAG

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|162165992|gb|FC341290.1|FC341290
EST:     GGATTACCTTCAGGATATAAACCCGGACATGGAGGTCATCAGCGTGTCTG                         GTAACTTCTGTGCGGAC
genomic: GGATTACCTTCAGGATATAAACCCGGACATGGAGGTCATCAGCGTGTCTGgtttgcaaca ... acatgtgcagGTAACTTCTGTGCGGAC
EST: gi|162177083|gb|FC353136.1|FC353136
EST:     GGATTACCTTCAGGATATAAACCCGGACATGGAGGTCATCAGCGTGTCTG                         GTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTC
genomic: GGATTACCTTCAGGATATAAACCCGGACATGGAGGTCATCAGCGTGTCTGgtttgcaaca ... acatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTC
EST: gi|162169988|gb|FC345928.1|FC345928
EST:     GGATTACCTTCAGGATATAAACCCGGACATGGAGGTCATCAGCGTGTCTG                         GTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTC
genomic: GGATTACCTTCAGGATATAAACCCGGACATGGAGGTCATCAGCGTGTCTGgtttgcaaca ... acatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTC

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: 23 (upstream exon), 17 (downstream exon)
Score: 6

GGTGACGCAATGGGGATGAACATGATATCCAAAGGCGTACAGAATGTTTTGGATTACCTTCAGGATATAAACCCGGACATGGAGGTCATCAGCGTGTCTGgtttgcaaca ... acatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctagcgcttgtttagctgtacagtatactcacgtagtctgtacatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG
                             tactcac  putative branch site (score: 6)
           ttgttta  TA-rich tract