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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatatagattcgtttttttaaatgttaggtctagcttatattggaaatgttttatcgcttattcagcgcagggttttaatatgcgtcttctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT

Basic information

species Physcomitrella patens
transcript PP1S272_13V6.5
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S272_13V6.5 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G134747_T01 (Zea mays), 3'ss of exon 1
------atatatagattcgtttttttaaatgttaggtctagcttatattggaaatgttttatcgcttattcagcgcagggttttaatatgcgtcttctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT
      ||  | || || |||  ||||  | | || |       |      | || ||  |       ||  |   |   | ||| |||  ||    |  |   ||  || | |||||   | | ||||  || || ||||||||||| ||||||||||| ||||||||||| || ||
gcttttatccagagctttgttagttta--tttcagtttatcagcactaacaagatattagaataacctttttgtcaacattgttactatatgt----tgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT

upper sequence: PP1S272_13V6.5 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G134747_T02 (Zea mays), 3'ss of exon 1
------atatatagattcgtttttttaaatgttaggtctagcttatattggaaatgttttatcgcttattcagcgcagggttttaatatgcgtcttctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT----------------------------
      ||  | || || |||  ||||  | | || |       |      | || ||  |       ||  |   |   | ||| |||  ||    |  |   ||  || | |||||   | | ||||  || || ||||||||||| ||||||||||| ||||||||||| || ||                            
gcttttatccagagctttgttagttta--tttcagtttatcagcactaacaagatattagaataacctttttgtcaacattgttactatatgt----tgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATGTAAGAGATACCAGTGCTTCATTTATGC
















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|162205230|gb|FC380912.1|FC380912
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162239982|gb|FC418785.1|FC418785
EST:     CGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67697134|gb|BJ957367.1|BJ957367
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67701145|gb|BJ961378.1|BJ961378
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67573748|gb|BJ946572.1|BJ946572
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67693986|gb|BJ954219.1|BJ954219
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67700516|gb|BJ960749.1|BJ960749
EST:     TGCGCTCATTCGGATNCCCACCGNTTGTGCAAGACCCTTACCATTTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: TGCGCTCATTC-GAT-CCCACCG-TTGTGCAAGACCC-TACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67692354|gb|BJ952587.1|BJ952587
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|18361453|gb|BJ193519.1|BJ193519
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162239983|gb|FC418786.1|FC418786
EST:     CGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67701515|gb|BJ961748.1|BJ961748
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|37842305|gb|BJ600313.1|BJ600313
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162219374|gb|FC396904.1|FC396904
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67508506|gb|BJ941371.1|BJ941371
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|208395581|gb|DC928996.1|DC928996
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67693480|gb|BJ953713.1|BJ953713
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162222811|gb|FC399065.1|FC399065
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67569108|gb|BJ941932.1|BJ941932
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162162852|gb|FC338101.1|FC338101
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67570694|gb|BJ943518.1|BJ943518
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGA
EST: gi|37850310|gb|BJ608318.1|BJ608318
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162246985|gb|FC424785.1|FC424785
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATATACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|18366564|gb|BJ198643.1|BJ198643
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|37849018|gb|BJ607026.1|BJ607026
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|208367515|gb|DC955695.1|DC955695
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162205229|gb|FC380911.1|FC380911
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|37846944|gb|BJ604952.1|BJ604952
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162161409|gb|FC337615.1|FC337615
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|67692348|gb|BJ952581.1|BJ952581
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
EST: gi|162247194|gb|FC420236.1|FC420236
EST:     CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAG                         GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA
genomic: CCGATGCGCTCATTCGATCCCACCGTTGTGCAAGACCCTACCATCTACAGgtaaaccttg ... ctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgttttatcgcttattcagcgcagggttttaatatgcgtcttctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT
                             ttttaat  putative branch site (score: 3)
                                     tgcgtcttcttttttt  CT-rich tract
                                           ttcttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatatagattcgtttttttaaatgttaggtctagcttatattggaaatgttttatcgcttattcagcgcagggttttaatatgcgtcttctttttttagGCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT

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