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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttcgtagggcaattttgaggtagttggtgccatgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG

Basic information

species Physcomitrella patens
transcript PP1S371_53V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 3'ss of exon 1
gttttcgtagggcaattttgaggtagttggtgcca--tgtgttacatcacttagcgctttgttatgtga-gttttaaatgatttttatttttc---caaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
        |  |    || |      ||  |  |   | | | || ||  | |     ||   |    | | || | ||| || | | || |     | ||||||||||| ||||||||||| ||||||||| ||||  | ||  |||||||||| ||  | || ||||| ||||||||||| || ||||||||||| ||||| ||
------ccaatgtttcttggctacgatttatttcgattatataacttccatgaaaaaatttccagaaaacgattgatatgcttctgaattattgtttacattgcagAGAAAGAGAATTTGTGTTTATATGGTCTTCCCAATGAGACATGGGAAGTGAACTTGCCTGCTGAGGAGGTTCCTCCAGAGCTTCCAGAACCAGCTCTGGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G008259_T02 (Zea mays), 3'ss of exon 2
---gttttcgtagggcaattttgaggtagtt-ggtgccatgtgttacatca-cttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
     |||| | |  |    ||    || || | |  ||||    | |  | |||  |     |   |  || | ||||  | |||| |  |||     |||||||||| |||||| |||| || |||||| ||||  | ||| |||||||||| ||  | || || || ||||||||||||||||||||||| || ||||| ||
cgaactttcctggtcctggattcttttaattagatagcatggaagaaaggatcttgacaaaaagaccta-gaatcttaa--ggttttgacgtttt--gtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
gttttcgtagggcaattttgaggtagttggtgccatgt--gttacatcacttagcgctttgttatgtga---gttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
       | ||   ||||| |  ||      ||||| |  | |  |   | |    |      |  |      ||  ||||  | |||  ||||       ||||||||||| ||||| || ||||||||  ||||  | ||  |||||||||||||  | || ||||| ||||||||||||||||| ||||| || ||||| ||
-----tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G153087_T01 (Zea mays), 3'ss of exon 2
gttttcgtagggcaat-tttgaggtagttggtgccatgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
 | ||  |       | ||||| ||      |   | || |    ||    |   ||            ||  | ||  | |||  ||||        ||||||||||||| || || ||||||||  ||||  | ||  |||||||| ||||  | || ||||||||||| ||||||||||| ||||| || ||||||||
-tcttgattcatttttgtttgaagtgagctattttaggtttagagtctgaaacaactgcaaataccttattcgagatattattttcttttgttttgcacagAGAAGGAGAACTTATGTTTATATGGACTTCCTAATGAGACATGGGAAATAAACTTGCCTGCTGAAGAGGTCCCTCCTGAACTGCCAGAGCCAGCTCTTGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G03160.2 (Glycine max), 3'ss of exon 2
----gttttcgtagggcaattttgaggtagttggtgccatgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
        |   |   || |||     || |   |   || |  |   |  || | |   |  |||| |||| |||| ||   | || ||||      || |||||||||||||||||||||||||||| |||||  | ||   |||||| |||||| |||| | |||||| |||||||| || ||||| || ||||  || ||
aggtagaattacaaatcattttatccatattaaat-ttattttctttgtagct-atcttatccttatatgagctttatatatctgttgttttattc--tttcagAGAAGGAGAATTTGTGCTTATATGGATTTCCTAATGAGCAATGGGAGGTAAATTTACCCGTTGAAGAAGTTCCTCCAGAGCTTCCTGAGCCTGTCCTAGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G00630.1 (Glycine max), 3'ss of exon 2
gttttcgtagggcaattttgaggtagttggtgcc---atgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
  | || |     |  |   |  |||   |  ||   | |  | |  |     || | | | |    || |||||       || | || |||    ||| ||||||||||||||||||  ||||||| |||||| | ||| |||||||||| ||| | || | ||| || || |||||||||||||| || || ||  | ||
--tgtccttcataatctcccaaataggaagaacccaaaagaatgattttttgaagtgttatttgcaatgtgttttgttaacattatgttattctcg-ttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
gttttcgtagggcaattttgaggtagttggtgcc-atgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttt-tccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
  | || |     |  |   |  |||   |  || | | |    ||   ||   |  || ||      || ||  || |   |||| || | |   ||| ||||||||||||||||||  ||||||| |||||| | ||| |||||||||| ||| | || | ||| || || |||||||||||||| || || ||  | ||
--tgtccttcataatctcccaaataggaagaacccaagagaatgattttttgaagtgttatttgcaatgtgttttattaacattatgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G42250.1 (Glycine max), 3'ss of exon 2
----gttttcgtagggcaattttgaggtagttggtgccatgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
        |   | | || ||||       ||      || |  |   |  || |     |  |||| |||| |||| ||   | || ||||      || |||||||||||||||||||||||||||| |  ||  | ||   ||||||||||||| |||| | |||||| |||||||| || ||||| || ||||  || ||
aggtagaattacaagtca-ttttatccctattaaatttattttctttgtagct-attttatccttatatgagctttatatatctgttgttttattc--tttcagAGAAGGAGAATTTGTGCTTATATGGATCACCTAATGAGCAATGGGAAGTAAATTTACCTGTTGAAGAAGTTCCTCCAGAGCTTCCTGAGCCTGTCCTGGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA16G00680.1 (Glycine max), 3'ss of exon 2
--------gttttcgtagggcaattttgaggtagttggtgccatgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
        |  ||  ||| |  |||   |||   ||  ||   ||| ||| ||    ||    |||| |   || |||||| |  ||   |    |||    || |||||||||||||||||||||| ||||| |||||    ||    |||||||||||| |||| |||||||| || || || || ||||| || || |  || ||
aggattaagaatttttagagggattgaaaggc--ttcctgtt-tgttttagatattata----tttggtgcttgtgttttaca-aatcaattcccttcattctttcagAGAAGGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAAATTTACCTGCTGAAGAAGTACCACCAGAGCTTCCTGAGCCCGTACTGGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G42790.1 (Arabidopsis thaliana), 3'ss of exon 2
gttttcgtagggcaattttgaggtagttggtgccatgtgt---tacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
||  |  | ||     |   |  |  ||  | |   || |   |   |   | |  | ||     |||| |||||  ||  ||   ||||       || |||||||||||||| | ||||| ||||| || ||  | |||| ||||||||| ||| ||||||||||||| || ||||||||  | ||||| || ||||||||
gtggttattggtattgtacaatatgatttatacttagtctctttgtgtggttaattgattaaagttgtgtgttttgtattgttacgatttg---ggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G20510.1 (Arabidopsis thaliana), 3'ss of exon 2
gttttcgtagggcaattttgagg--tagttggtgccatgtgttac--atcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
||      |   |  |||    |  || || ||  | |    | |  || |  ||||| ||  | |  |||  |||  |||| |    ||||   | ||| |||||||| ||||| | ||||| ||||| || ||| | ||||  |||||||| ||  ||||||||||||| || |||||||| ||||| |||||||| || ||
gtagctaaatatcgttttcagagagtatttcgttgctttctctgctaattaagtagcg-ttgataaactgaagtttgtatgact---gttttatgacatttcagAGAAGCAGAATCTCTGCTTGTATGGATTCCCAAATGAAGTGTGGGAAGTTAACTTACCAGCTGAAGAAGTGCCTCCTGAGCTTCCCGAACCTGCACTCGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G26210.1 (Arabidopsis thaliana), 3'ss of exon 2
gttttcgtagggcaattttgaggtagttggtgccatgtgttacatcactt-agcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
||     | | ||    |  | || |||| |    ||| | || |   || |       ||| | |||    |        |||   |||    |||  ||| ||||||||  | ||| | || ||   |||| | ||    |||||||| ||| | ||||||||||||||||||||||| || ||||| ||||   | ||
gtagagtttgagcggagtcaaagt-gttgattttttgtttgacttggttttaatttaaggttttttgaacaattgtcatcattttccttttgtgattatagAAAAGGAGAACCTTTGCCTTTACGGACATCCAAATGAGCACTGGGAAGTGAATTTGCCAGCTGAAGAGGTTCCTCCTGAGCTCCCAGAGCCTGTCTTGGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------gttttcgtagggcaattttgaggta-gttggtgccatgtgttacatcacttagcgctttgttatgtgagtttta---aatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
                                                                                |||    | |     | ||||  |  ||||||   |    ||   | | ||||  ||    | ||||  ||||    || |  ||| ||| ||    || | ||||||||||||||||||  | |||||  ||||| | ||  ||||||| || |||||||| | ||| || ||||||||||| ||||| ||||| ||| | ||
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggt--taaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttat-gtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG

upper sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv09s0002g01600.t01 (Vitis vinifera), 3'ss of exon 2
gttttcgtagggcaattttgaggtagttggtgccatgtgttacatcacttagcgctttgttatgtgagttttaaatgatt-tttat-ttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
  |   | |      ||  ||  |      | |||  | |||   |    ||  ||   || | ||| ||| |  ||  |   | | |||| ||  || |||||||||||||| ||||| | ||||| |||||| | |||  ||||||||| ||| |||| || |||||||| ||||| ||||| ||||| ||||| || ||
--tacagaatcttgtttcggatatgagatattccagctcttattcctagaaggcctgccttctatgattttaacttggctacatgtattttgcaccttacagAGAAGGAGAATCTGTGCCTTTATGGATTTCCAAATGAACTATGGGAAGTCAATTTACCTGCAGAAGAGGTGCCTCCAGAACTCCCAGAGCCTGCACTAGG

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|162221663|gb|FC397888.1|FC397888
EST:     ACGTGGAAGAGTTTTACCGCCAATGTGATCCAG                         AGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAA
genomic: ACGTGGAAGAGTTTTACCGCCAATGTGATCCAGgtgcgaaatg ... caaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAA
EST: gi|67570731|gb|BJ943555.1|BJ943555
EST:     ACGTGGAAGAGTTTTACCGCCAATGTGATCCAG                         AGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAA
genomic: ACGTGGAAGAGTTTTACCGCCAATGTGATCCAGgtgcgaaatg ... caaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAA
EST: gi|162169023|gb|FC345705.1|FC345705
EST:     ACGTGGAAGAGTTTTACCGCCAATGTGATCCAG                         AGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAA
genomic: ACGTGGAAGAGTTTTACCGCCAATGTGATCCAGgtgcgaaatg ... caaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAA
EST: gi|100448621|gb|CJ972920.1|CJ972920
EST:     ACGTGGAAGAGTTTTACCGCCAATGTGATCCAG                         AGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAA
genomic: ACGTGGAAGAGTTTTACCGCCAATGTGATCCAGgtgcgaaatg ... caaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG
                                 tttttatttttcc  CT-rich tract
          tttgttatgtgagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttcgtagggcaattttgaggtagttggtgccatgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG