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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactttgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG

Basic information

species Physcomitrella patens
transcript PP1S62_236V6.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 3'ss of exon 3
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactttgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG----
                   |     ||   || | |||  ||    |  | ||  | |   ||||||||            ||   || || | || |  ||              |||||| ||||||||||||||||| |||||||||||||| |||||  || | ||||| || || ||||| || ||  |     
-------------------gtatattctgctttctctagtattt--ttctactacttcccttcatcatgt-----------aacatcccctgtaattttgac--------------acagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAA

upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os04g45970.2 (Oryza sativa), 3'ss of exon 3
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactttgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG
                   |     ||   || | |||  ||    |  | ||  | |   ||||||||            ||   || || | || |  ||              |||||| ||||||||||||||||| |||||||||||||| |||||  || | ||||| || || ||||| || ||  | 
-------------------gtatattctgctttctctagtattt--ttctactacttcccttcatcatgt-----------aacatcccctgtaattttgac--------------acagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATA

upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G427097_T01 (Zea mays), 3'ss of exon 3
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactt-tgtttttgt-acagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG
                             ||    |||||||  | | ||| |  |   | |  | ||||||||        | |   | | | || |  ||   || ||   |||| |||||| ||||| |||||  |||| ||||||||||||||||||||  |  | || || ||||| ||||| || ||  | 
-----------------------------gtaggcctaacattgctt-ttgttatttttttttgt-atgctcagct------atcttgtttttcatttgtaccttttatgcaattgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATA

upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G427097_T02 (Zea mays), 3'ss of exon 3
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactt-tgtttttgt-acagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG-------------------------
                             ||    |||||||  | | ||| |  |   | |  | ||||||||        | |   | | | || |  ||   || ||   |||| |||||| ||||| |||||  |||| ||||||||||||||||||||  |  | || || ||||| ||||| || ||  |                          
-----------------------------gtaggcctaacattgctt-ttgttatttttttttgt-atgctcagct------atcttgtttttcatttgtaccttttatgcaattgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATAGTAAGTGAAAAAATGTGGCAGCAAG

upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv16s0039g02750.t01 (Vitis vinifera), 3'ss of exon 3
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactttgtt--tttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG
                                                ||     |  ||||  | |  |||     | |    | | |   |||     |    ||| |   | ||  ||||||||||| |||||||||||||||||||| ||||| |||||  |  | |||||||| || ||||| || ||  | 
-----------------------------------------------gttatcttt-tgtct-gtaacactcttgaaatattctctcattcatgaagctgaaatatttataaatatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATA

upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv16s0039g02720.t01 (Vitis vinifera), 3'ss of exon 3
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctct----gatctcaacgactt-tgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG
                                                     | |   | |  ||     || |   || | |  | ||  |    || || ||  | || |   | ||  ||||||||||| |||||||| ||||||||||| ||||| |||||  |  | ||||| || || ||||| || ||  | 
-----------------------------------------------------gttatcttttgtctgtaacactcttgaaatattcttcattcatggaactgaaatatttataaatatgagcagACTATGGCATGGATTTTCGACGAGTACTCAAAATTCCATGGTCACTCACCGGCTGTAGTGACTGGAAAGCCAATA

upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcat---gctcagtgcagagaaacccctctctgatctcaacgactttgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG
                         |  | || ||||    |    | || ||  |   | ||||  |   | |   |  | | |      | | |  | |       || |||| |  |||||| |||||||||||| |||| |||||||| || |||||||||||  |||| || || || ||||| || ||  | 
-----------------------gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttattttt------ttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT

upper sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactttgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG
                             |||    |  | |    | ||| |  | | | || |     |   |||| ||         |    | |||     ||||||| |  |||||| |||||||||||| |||| |||||||| || |||||||||||  |||| || || || ||||| || ||  | 
-----------------------------gttttttt--ctttttcttttgttctttc-tttcttttctttttttgcaaag--------ttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT

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|162167228|gb|FC342793.1|FC342793
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|208345526|gb|DC909216.1|DC909216
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTGGGATTTTGGACG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACG
EST: gi|162176130|gb|FC351079.1|FC351079
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|162253971|gb|FC430215.1|FC430215
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|67573617|gb|BJ946441.1|BJ946441
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|162275836|gb|FC451397.1|FC451397
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|162162143|gb|FC337717.1|FC337717
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|162194068|gb|FC370243.1|FC370243
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|100396442|gb|BY990131.1|BY990131
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|162151269|gb|FC327723.1|FC327723
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCG
EST: gi|18346137|gb|BJ178180.1|BJ178180
EST:     TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAG                         ACTATGGCTTGGATTTTGGA
genomic: TCGGTCCTCATCTTGACATCCCAGCCCCGGACATGGGTACCAATGCTCAGgtatgttccg ... ttttgtacagACTATGGCTTGGATTTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgctcagtgcagagaaacccctctctgatctcaacgactttgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG
                        ctctgat  putative branch site (score: 4)
                                       ctttgttttt  putative PPT
                                        tttgttttt  TA-rich tract