Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAATTGGCCATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgatttaggttctcgttggtttattatttttctttctctgggcggccttcatttttttcttcttatttttattttatttttttccttttccttttggaagttggttgattttagaaatggtgagaatcggcttttacgtttttgagtaaattctgttgtgctcttcttcggagcag

Basic information

species Physcomitrella patens
transcript PP1S207_94V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 3
GTACAATTGGCCATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgatttaggttctcgttggtttattatt--tttctttctctggg--cggccttcatttttttcttcttatttttattttatttttttccttttccttttggaagttggttgattttagaaatggtgagaatcggcttttacgtttttgagtaaattctgttgtgctcttcttcggagcag
|||| ||||||||||||||||| || ||||| || || || || || ||||||||||| ||||| ||||| | ||  ||    || || ||||  ||||   |  ||    ||   ||  | |||    ||   ||| | | | || ||| |   | |  ||||                                                                                 
GTACCATTGGCCATGTGGCTCATGGAAAGTCCACTGTTGTTAAAGCTATATCTGGTGTTCAGgtgtgattcatgtattc--cagtgtaatatttgtttcaaacattgaatccgagttttgtatttggtgtcaattttatgtgtcatctttctgtatcttttttt---------------------------------------------------------------------------------

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G117900_T01 (Zea mays), 5'ss of exon 3
GTACAATTGGCCATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgatttaggttctcgttggtttattatttttcttt---ctctgggcggccttcatttttttcttcttatttttattttatttttttccttttccttttggaagttggttgattttagaaatggtgagaatcggcttttacgtttttgagtaaattctgttgtgctcttcttcggagcag
|||| ||||||||||||||||| || ||||| || || |||||||| ||||| || || ||||| ||||| |  |  ||  | || || ||||| | ||    |  ||||      |||| | |||  | | | |||||| |    | ||||  | ||   ||                                                                                 
GTACCATTGGCCATGTGGCTCATGGAAAGTCTACTGTTGTGAAGGCTATATCCGGAGTTCAGgtgtgattcacatattc--tagtataatatttgttttcaagcattgggtccaagtcatgtctttggtgtcagttttatgtgtcatctttctgtatctgctta--------------------------------------------------------------------------------

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 5'ss of exon 2
GTACAATTGGCCATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgatttaggttctcgttggtttattatttttctttctctgggcggcct-tcatttttttcttcttat----ttttattttatttttttccttttccttttggaagttggttgattttagaaatggtgagaatcggcttttacgtttttgagtaaattctgttgtgctcttcttcggagcag
| |||||||| ||||||||||| |||||||| ||||| || || || ||||||||||| ||||| |  |||   || |  | ||||| || |||   |||  |   ||    | | | |||| | |  |||      || | | ||  ||| |  | |  |                                                                                     
GCACAATTGGTCATGTGGCTCATGGGAAGTCCACAGTTGTAAAAGCTATATCTGGTGTTCAGgtgttttttttttttttttgggtttcttttttgaatttaacactgctttttattagttttatttctttagaagagttgagtgtaaatttgtattgtcacc------------------------------------------------------------------------------------

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 5'ss of exon 3
GTACAATTGGCCATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgatttaggttctcgttggtttattatttttctttctctgggcggccttcatttttttcttctta----tttttattttatttttttccttttccttttggaagttggttgattttagaaatggtgagaatcggcttttacgtttttgagtaaattctgttgtgctcttcttcggagcag
| ||| |||| |||||||| || |||||||| ||||| || || |||||||||||||| |||||   |||| | |||| ||| |  | | | | ||   |  |||   |   ||  ||||  | |  |||      || | | ||  ||| | || |  | ||                                                                                  
GCACAGTTGGGCATGTGGCACATGGGAAGTCCACAGTTGTAAAAGCCATATCTGGTGTTCAGgttatattttgcttcttgtttgcatttgaatatttaata-ctgcttgttattagttttcatttctttagaagccttgagtataaatttgtactgtcacatt----------------------------------------------------------------------------------

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|100363156|gb|BY984385.1|BY984385
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18367900|gb|BJ199983.1|BJ199983
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18358005|gb|BJ190064.1|BJ190064
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|208390337|gb|DC929285.1|DC929285
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|67702207|gb|BJ962440.1|BJ962440
EST:     ATGTGGCTCACGGGAAGTCTACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTT
EST: gi|100364249|gb|BY984518.1|BY984518
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|162195753|gb|FC371144.1|FC371144
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|208367353|gb|DC939869.1|DC939869
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18328485|gb|BJ160490.1|BJ160490
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|100361446|gb|BY984092.1|BY984092
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18360577|gb|BJ192640.1|BJ192640
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|100421143|gb|BY976096.1|BY976096
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18330481|gb|BJ162487.1|BJ162487
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18346238|gb|BJ178281.1|BJ178281
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGGGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18358858|gb|BJ190917.1|BJ190917
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18326535|gb|BJ158534.1|BJ158534
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18364125|gb|BJ196198.1|BJ196198
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18350306|gb|BJ182357.1|BJ182357
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|67571651|gb|BJ944475.1|BJ944475
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|67717529|gb|BJ967788.1|BJ967788
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18357875|gb|BJ189934.1|BJ189934
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGGGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|67702081|gb|BJ962314.1|BJ962314
EST:     ATGTGGCTCACGGGAAGTCTACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|208391361|gb|DC941811.1|DC941811
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|162262330|gb|FC437657.1|FC437657
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|18361296|gb|BJ193362.1|BJ193362
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|67703591|gb|BJ963824.1|BJ963824
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|100448476|gb|CJ972775.1|CJ972775
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
EST: gi|100365464|gb|BY966609.1|BY966609
EST:     ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAG                         ACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT
genomic: ATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGT

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: 34 (upstream exon), 30 (downstream exon)
Score: 30

GTACAATTGGCCATGTGGCTCACGGGAAGTCGACAGTAGTGAAGGCCATATCTGGTGTGCAGgtatgattta ... ttcggagcagACCGTCCGATTCAAGAACGAGTTGGAGAGGAATATCACCATTAAGCTGGGTTATGCCAACGCCAAAATCTACAAGTGTGAAGATGAGCGCTGTCCTCGAC




<











<


<