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

...gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA

Basic information

species Physcomitrella patens
transcript PP1S85_168V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 3
--gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
   |  |  | | ||    | ||||      |  | |  |   || | ||  | | |  |||||    || | |   |     ||    |  |    |||||||||||||||| || || ||||||||||| || |||||||||||  ||||||| ||||| ||| | || || || || |||||||||||||||   || |
tttttaattctattaccagtctgcaagcacatctgat--tatctaatctgacatgtacatttagttttcattcatcttagtgatacaaatcatttaccgcagGTTGATTATGCATGTACCCCAGAAGAAGTGCAGCAGCATTTTCAAGCGTGTGGCACAGTCAATAGAGTGACGATCTTAACTGACAAGTTTGGACAGCCAA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM5G862331_T04 (Zea mays), 3'ss of exon 3
gtacacgcaac-tatgtttatgcagcagtttaaggtcctgcgtactttgtgaagg--aattttagcgaacacttagtctgagtttat-tgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
 |  | |  ||  ||  || |  |||  |  |      ||  |||   | | ||   |   | ||  |||||    | |||  | ||    |  ||    |||||| |||||||| ||||| ||||||||||| ||||||||||| ||  | ||||| || || ||  | || ||||| ||||||||||||||||||   || |
-ttaatgggacacatagtt-tctagccttacatttctgtgtctacccagagcagtccacactaagttaacacc--atttgaactgatacaatcatgtactgcagGTGGATTATGCTTGCACCCCAGAAGAAGTGCAACAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGACAGCCAA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
-----gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaatt-ttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
     ||       | |    | | |||   ||||  || | | | |  | ||| |   | || | ||  | || ||   ||||    ||  | |       ||||||||||||||| ||||| ||||||||||| || |||||||| ||  | ||||| || || ||  | || ||||| |||||||||||||||||    || |
taggcgtgttgcttaatgacataacgca-tggtttgtggccttacat-ttctgttatccatttgtcagtcagcattttaactgatgcaatcatatac----tgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G082198_T01 (Zea mays), 3'ss of exon 3
--------gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
         ||   | |  ||||| |||    ||| |    |      | | | ||| |    |||  |  | |  || ||| |  || || ||   |  ||   |||||||| ||||| ||||||||||||||||| || ||||||||  | || ||||| || |||||  | || |||||  ||||||||||||||||   ||| |
tcgaagttttatttgtatatatgtctatttgtcagctgtttggttattgaaatatgtaac---attacaa-gtatgctcagtttcggtgtaatgg--caact--acagGTTGACTATGCATGCACTCCAGAAGAAGTGCAGCAGCATTTCAATTCTTGTGGAACTGTTAACAGAGTGACAATCCTGACTGACAAGTTTGGGCAACCAA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
gtacacgcaactatgttta-tgcagcagtttaaggtcctgcgtactttgtgaaggaatt-ttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
 |  |      |||| | | || | ||| || | | ||    |   ||   | |  ||| || |||   |       |||  ||    ||| || ||  |||||||||||||| ||||| ||||||||||| || || || |||||||| |||||||| || ||  | ||||| ||  ||||||||||||||||    || |
atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattg--atttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G06030.1 (Glycine max), 3'ss of exon 3
gtacacgcaactatgtttatgcagcagtttaaggtcctgcgta-ctttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
 |    |  |  |  |   ||||    |   |  |  | | || |  | |    |     | ||   ||  || ||| | |  |||   | | || | ||||| || ||| | |||||||| |||||||| ||||||||||||||||| ||||| ||||| ||  | ||||| |||   ||||| ||||||||   |||||
tttggtgttaacagatacttgcaaacatagtacttttttcatatcactttacttgttgcattgctctcatataatctca-tggatttgatgttctccacagGTGGACTATTCATGCACTCCTGAAGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAGTCACCATTCGAACTGATAAGTTTGGCCAACCCA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
gtacacgcaactatgttta-tgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattg-tttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
     |     |||| | | || | ||  || | | ||  | |      | |    || |||  |    |  |  |       |||| ||| || ||  |||||||||||||| ||||| ||||||||||| || || || |||||||| |||||||| || ||  | ||||| ||  |||| |||||||||||    || |
--tttctttcttatgataactgaatcaagtttaagccccccttttggattaacatgatattattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G18970.1 (Glycine max), 3'ss of exon 3
gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttg--tgaaggaatttta--gcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
       ||  ||  |  |  ||  ||| | | ||  ||  | |||||  |  |    ||  |  ||   ||| || |||  ||  |||   | | || | ||||| || ||| | |||||||| || ||||| ||||||||||||||||| ||||| ||||| ||  |  |||| |||   ||||| ||||||||   |||||
--gttaacagatacttgaaaaca-tagtatcatgtggtgaatgctttggctttacttgttgcattgctctcacataatctt-gtggatttgatattctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAATCACCATTCGAACTGATAAGTTTGGCCAACCCA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ10007 (Selaginella moellendorffii), 3'ss of exon 2
gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagt-ctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
                                      |     ||| |       | ||  ||    ||| |  || |||   | || | | |||   |||| |||||| | ||||| ||||| ||||| |||||||| ||||| || ||||| || ||||| || || || ||||| ||||||||||| |||   ||||
--------------------------------------gtaagttttcttttcttctcttctcgttgccttggaacttagtgagtggtatgttctt---agGTGGATTATTCGTGCACACCAGAGGAAGTCCAACAGCACTTTCAATCCTGTGGCACTGTTAACCGGGTTACTATTTTAACTGACAAGTTCGGACAGCCCA

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|67578985|gb|BJ951136.1|BJ951136
EST:     TGATGCGCGTTCAGTTTTTGTTGGGGAAT                         GTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTG
genomic: TGATGCGCGTTCAGTTTTTGTT-GGGAATgtaaacactc ... tgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTG
EST: gi|18363019|gb|BJ195091.1|BJ195091
EST:     ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAAT                         GTTGATTATGCCTGCACT
genomic: ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAATgtaaacactc ... tgcttcgcagGTTGATTATGCCTGCACT
EST: gi|67507705|gb|BJ940585.1|BJ940585
EST:     ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAAT                         GTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGT
genomic: ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAATgtaaacactc ... tgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGT
EST: gi|67578551|gb|BJ950718.1|BJ950718
EST:     ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAAT                         GTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGT
genomic: ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAATgtaaacactc ... tgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
                                         tttctgcttc  CT-rich tract
                                  tttattgttt  TA-rich tract