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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcccttggatttttctcagttgtactggtcctcttaccaaattttgcttgcctttcgtcacgatgcatggttgaccttaaagcgtgttgaaaaccatttttgtgttcaatagtaatccagattgtctttgctcttcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATTGCAAGGAGGACGCCAGGGTTCACCGGTGCCGACTTACAAAACTTGATGA

Basic information

species Physcomitrella patens
transcript PP1S10_192V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S10_192V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacttcccttggatttttctcagttgtactggtcctcttaccaaattttgcttgcctttcgtcac-gatgcatggttgaccttaaagcgtgttgaaaaccatttttgtgttcaatagtaatccagattgtctttgctcttcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATTGCAAGGAGGACGCCAGGGTTCACCGGTGCCGACTTACAAAACTTGATGA
                                                     | | |||| |  | | |  ||    |    |     || |    |   || |   || |   || |  ||   || |  |||| | ||    |||||||||| ||| | || ||| || | |  || ||||| |||||||| ||| |||| || ||||| || || ||||| ||||| |||||||||||| ||||||
----------------------------------------------------gttcttttcatagctgttttataaaggttactggtttgtctatggagttatgtgaatgattcttatttctctctatggggtttggttttat--tttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTTGCCAGAAGGACCCCTGGTTTCACGGGTGCTGACTTACAAAACCTGATGA

upper sequence: PP1S10_192V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 1
gtacttcccttggatttttctcagttgtactggtcctcttaccaaattttgcttgcctttcgtcacgatgcatggttgaccttaaagcgtgttgaaaaccatttttgtgttcaatagtaatccagattgtctttgctcttcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATTGCAAGGAGGACGCCAGGGTTCACCGGTGCCGACTTACAAAACTTGATGA
                                             | |   | | | |||  | |   | ||| | |||  ||    |     ||| |   | ||| ||    ||| |  | || |   |   |  |  |       |||| |||||  | || ||| || | ||||||||||| |||||||| |||||||| || ||||| ||||| ||||| || || ||||| || ||| ||||||
--------------------------------------------gaatgaccatacattt-atgaaagttcattgatgatttttggtcaga--gaagagtttcttt-tggctgataatgttgca-accattgatatttctgtatgacagGTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATTGCGAGAAGGACCCCAGGCTTCACAGGGGCTGACTTGCAGAACCTGATGA

upper sequence: PP1S10_192V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ31931 (Selaginella moellendorffii), 3'ss of exon 1
gtacttcccttggatttttctcagttgtactggtcctcttaccaaattttgcttgcctttcgtcacgatgcatggttgaccttaaagcgtgttgaaaaccatttttgtgttcaatagtaatccagattgtctttgctcttcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATTGCAAGGAGGACGCCAGGGTTCACCGGTGCCGACTTACAAAACTTGATGA
                                                                                          ||  |     | |||||    |  |  || |   | || ||||| || || |  || |||| || |||   || ||  |  ||| |||||||||||||||||||||||| ||||| || || ||||| || ||||| || ||||| |||||| | ||||
------------------------------------------------------------------------------------------gtaaagctgaagttttgataacgttcttacttacgtttttcttttct-tttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATCGCAAGAAGAACTCCAGGCTTTACCGGCGCGGACTTGCAAAACCTCATGA

upper sequence: PP1S10_192V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ37923 (Selaginella moellendorffii), 3'ss of exon 1
gtacttcccttggatttttctcagttgtactggtcctcttaccaaattttgcttgcctttcgtcacgatgcatggttgaccttaaagcgtgttgaaaaccatttttgtgttcaatagtaatccagattgtctttgctcttcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATTGCAAGGAGGACGCCAGGGTTCACCGGTGCCGACTTACAAAACTTGATGA
                                                                                          ||  |    || |||||  |    |  | |   |  || || ||    || |  || |||| || |||   || ||  |  ||| |||||||||||||||||||||||| ||||| || || || || || ||||| || ||||| |||||| | ||||
------------------------------------------------------------------------------------------gtaaagctgcagttttg-ataacgttcttacttacgttttccttttcttttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATCGCAAGAAGAACTCCGGGCTTTACCGGCGCGGACTTGCAAAACCTCATGA

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|162221326|gb|FC398110.1|FC398110
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162155045|gb|FC330839.1|FC330839
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTG
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTG
EST: gi|162174837|gb|FC351629.1|FC351629
EST:     GGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: GGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162195965|gb|FC372669.1|FC372669
EST:     AGGTCACCGTCTACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162156477|gb|FC332085.1|FC332085
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|100439117|gb|BY980102.1|BY980102
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|100440729|gb|BY980549.1|BY980549
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162169037|gb|FC345719.1|FC345719
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162195503|gb|FC369867.1|FC369867
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162175075|gb|FC351962.1|FC351962
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162162315|gb|FC339124.1|FC339124
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162266406|gb|FC443261.1|FC443261
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162169121|gb|FC346011.1|FC346011
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAA
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAA
EST: gi|162154060|gb|FC330295.1|FC330295
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAAGAT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAA-GAT
EST: gi|162214909|gb|FC390469.1|FC390469
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162188880|gb|FC364894.1|FC364894
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162150058|gb|FC326589.1|FC326589
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTG
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTG
EST: gi|162209689|gb|FC386188.1|FC386188
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162152370|gb|FC328557.1|FC328557
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
EST: gi|162206306|gb|FC382584.1|FC382584
EST:     AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAG                         GTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT
genomic: AGGTCACCGTCGACAGGCCAGATGTTCAAGGGCGTGTTAGGATTCTTCAGgtacttccct ... tcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaccatttttgtgttcaatagtaatccagattgtctttgctcttcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATTGCAAGGAGGACGCCAGGGTTCACCGGTGCCGACTTACAAAACTTGATGA
                                ttgtctttgctcttcc  CT-rich tract
                  aatagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttcccttggatttttctcagttgtactggtcctcttaccaaattttgcttgcctttcgtcacgatgcatggttgaccttaaagcgtgttgaaaaccatttttgtgttcaatagtaatccagattgtctttgctcttcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATTGCAAGGAGGACGCCAGGGTTCACCGGTGCCGACTTACAAAACTTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA