Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatatcttctcgtagttagttcaaaatcagctctcgatcatttataatgatgaatcatctggctgttggttgttgatgataatgcatgcactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGTTGTGACAAGCAAGCAAAAATGTGGCCCATACTATCTGGTGGCCAGGCAG

Basic information

species Physcomitrella patens
transcript PP1S33_129V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S33_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 4
aaaatatcttctcg-tagttagttcaaaatcagctctcgatcatttataatgatgaatcatctggctgttggt-tgttgatgataatgcatgcactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGTTGTGACAAGCAAGCAAAAATGTGGCCCATACTATCTGGTGGCCAGGCAG
    |||  ||||  || ||   |||| | ||  |    || || || | |  ||| |   || |   || || || | ||  | ||   |   || |  ||||| | || || || |||||||| ||||||| ||| |||||||| ||||| ||||| || |||| ||||||||||||  |  | |||||||| |||||  
---gtatgatctcaatatttctctcaagaccacattcacataatgtacagtattgattttcctagtatttagtgtgctcat--tgatttgttttctat-cagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGCTGTGATAAACAAGTAAAAATGTGGCCTCTGTTGTCTGGTGGGCAGGCTC

upper sequence: PP1S33_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 4
aaaatatcttctcgtagttagttcaaaatcagctctcgatcatttataatgatgaatcatctggc-tgttggttgttgatgata-----atgcatgcactt---tgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGTTGTGACAAGCAAGCAAAAATGTGGCCCATACTATCTGGTGGCCAGGCAG
    |||  |||    |||   |   |        |  ||    |     | |  ||  |||  | ||| | ||||   || ||     ||  ||    ||   | |||||  | ||||| || |||||||| ||||||| ||| || ||||| ||||| ||||||||||| |  |||||||||||  | || || ||||| ||| |  
---gtatgatcttagtgttttctgggatatgttaatatatttgattgggcggtagattgtcttccatgtagtttgtatctggtatcctcattgatttgtttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGCTGTGACAAGCAGGTCAAAATGTGGCCTCTTCTGTCAGGTGGGCAGCCTC

upper sequence: PP1S33_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 4
aaaatatcttctcgtagttagttcaaaatcagc--tctcgatcatttataatgatg-aatcatctggctgttggttgttgatgataatgcatgcacttt----gtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGTTGTGACAAGCAAGCAAAAATGTGGCCCATACTATCTGGTGGCCAGGCAG
  || |  || |  || ||  | |||||||  |  | |   | |||| |  |  |      || |   | |||| | || |   |  | ||||   |||    ||||||  |||||||||| |||||||| |||||||  || || ||||| ||||| |||||||||||||  |||||||||||  |  | ||||| || ||  |  
gtaacaaattattctatttt-tacaaaatctacatttttatttatttttctttttttggaaatttttgttttggattttaaatttggtacatgttatttttgtgtagGTTCTATGCTCTGCTTGGAAGGATGATGGAACAACTGTCTTCTCTGGAGGCTGTGACAAGCAAGTGAAAATGTGGCCTTTGTTGTCTGGCGGGCAACCTA

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|208345666|gb|DC909597.1|DC909597
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208383584|gb|DC903541.1|DC903541
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100434529|gb|BY960765.1|BY960765
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208392008|gb|DC941856.1|DC941856
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208355495|gb|DC942615.1|DC942615
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100370102|gb|BY967519.1|BY967519
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCCGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100434093|gb|BY978955.1|BY978955
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100364164|gb|BY966747.1|BY966747
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208353800|gb|DC906488.1|DC906488
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100433091|gb|BY978805.1|BY978805
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100414674|gb|BY956808.1|BY956808
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208350426|gb|DC906128.1|DC906128
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100378469|gb|BY968614.1|BY968614
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCCCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208346265|gb|DC905240.1|DC905240
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100352940|gb|BY945526.1|BY945526
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208393843|gb|DC938454.1|DC938454
EST:     NGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100427817|gb|BY959139.1|BY959139
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208357300|gb|DC910683.1|DC910683
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|208358353|gb|DC934546.1|DC934546
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100364263|gb|BY984525.1|BY984525
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100369219|gb|BY985069.1|BY985069
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100359430|gb|BY984250.1|BY984250
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|162172691|gb|FC348072.1|FC348072
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
EST: gi|100378001|gb|BY949630.1|BY949630
EST:     AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCT                         GTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT
genomic: AGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGT

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), 33 (downstream exon)
Score: 5

GTGAGGTGCTGGGAGATTCAGTCAAATGGCAGCAGTGTTCCTAAAGCAGCTATTTCACATGAATCGCCTgtaagtgtag ... cactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGTTGTGACAAGCAAGCAAAAATGTGGCCCATACTATCTGGTGGCCAGGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgatgaatcatctggctgttggttgttgatgataatgcatgcactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGTTGTGACAAGCAAGCAAAAATGTGGCCCATACTATCTGGTGGCCAGGCAG
                           tgttgat  putative branch site (score: 5)
                                atgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatatcttctcgtagttagttcaaaatcagctctcgatcatttataatgatgaatcatctggctgttggttgttgatgataatgcatgcactttgtagGTCTTATGCTCTGCCTGGAAGGAGGATGGAAGTACAGTGTTCTCAGGAGGTTGTGACAAGCAAGCAAAAATGTGGCCCATACTATCTGGTGGCCAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG