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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtggaagcgtgatgcagttctccaataaatcttgagatttggtccattgtattagcgcagctgtaagcacggagggttcatgcacggccattcccttacagcacttggctcctcattgtggttgttgtgattgtatgatgtattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTTGGACCTGCTGCAAATCGATTGCTGGATTCTTATAGCCAATTGCTTAAG

Basic information

species Physcomitrella patens
transcript PP1S216_69V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S216_69V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G07390.1 (Glycine max), 3'ss of exon 8
gtacagtggaagcgtgatgcagttctccaataaatcttgagatttggtccattgtattagcgcagctgtaagcacggagggttcatgcacggccattcccttacagcacttggctcctcattgtggttgttgtgattgtatgatgtattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTTGGACCTGCTGCAAATCGATTGCTGGATTCTTATAGCCAATTGCTTAAG
                                             | |||| |   ||     |  | |     |  | | ||     |     |||   | |  |       ||| | ||    |  |  |    |  |  ||   ||| | |||||||||| ||||||||||| |||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||  ||||  | ||||      |  | |||
---------------------------------------------gttccaat---ttgagatacttat-----ctaatgattttattatactaatta--taatggtggcatactcataatatctggggaagcttataaaaaattgcttgtgtagGAAATTCGTCCATGGACGCACATGATGGAGGTTCCGCAACTTCATGGATTTGGACCAGCTGCCAATCGTTTATTGGAGGCCTATAAAATGCTTTTGAAG

upper sequence: PP1S216_69V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G17620.1 (Arabidopsis thaliana), 3'ss of exon 7
gtacagtggaagcgtgatgcagttctccaataaatcttgagatttggtccattgtattagcgcagctgtaagcacggagggt-tcatgcacggccattcccttacagcacttgg----ctcctcattgtggttgttgtgattgtatgatg-tattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTTGGACCTGCTGCAAATCGATTGCTGGATTCTTATAGCCAATTGCTTAAG
                                                            ||||        | | ||   | | |||  | | |  ||  || ||| |  ||          | ||||   | || | | | | |   |   ||   ||||||||||| |||||||||||||||||||| || || |||||||||||  |||| ||||||||||| || || || ||  | ||||      |  | |||
------------------------------------------------------------cgcaaaaaatgcctctgaatatcttatgatctgactatcttttccagaaactgaaaaataagccgttgtatct-ttatcactatgtttggacttttttcagGAAATTCGTCCATGGACGCATATGATGGAAGTGCCTCAGCTTCATGGTTTTGGTCCTGCTGCAAACCGTTTACTAGAAGCATATAATATGCTTTTAAAG

upper sequence: PP1S216_69V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv15s0024g01470.t01 (Vitis vinifera), 3'ss of exon 7
gtacagtggaagcgtgatgcagttctccaataaatcttgagatttggtccattgtattagcgcagctgtaagcacggagggttcatgcacggccattcccttacagcacttggctcctcattgtggttgttgtgattgtatgatgtattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTTGGACCTGCTGCAAATCGATTGCTGGATTCTTATAGCCAATTGCTTAAG
                                                         |  |     | |   |||  |    || | | | |  | |   |||| |      |    || | ||  ||   |   || |  | ||  ||  | |||||||||| || ||||| || |||||||| || || |||||||||||  ||||||| ||||| ||||| ||| ||||  | || |      |  | |||
--------------------------------------------------tccaagctcacatccatcttgacaccaaataatctttccctgatact---ttactgtgaacagtctgtcttcgtaattacagcattttt--ggtggtttttgtagGAAATTCGCCCTTGGACTCACATGATGGAGGTACCACAGCTTCATGGGTTTGGACCAGCTGCCAATCGCTTGTTGGAGGCGTACAAGATGCTTTTGAAG

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|208377606|gb|DC922709.1|DC922709
EST:     TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAG                         GAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
genomic: TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAGgtacagtgga ... tattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
EST: gi|162265700|gb|FC443106.1|FC443106
EST:     TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAG                         GAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
genomic: TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAGgtacagtgga ... tattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
EST: gi|208364455|gb|DC958024.1|DC958024
EST:     TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAG                         GAAATTCGGCCATGGACGCATATGATGGACGTTCCCTAGCTTCATGGACTT
genomic: TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAGgtacagtgga ... tattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
EST: gi|162265701|gb|FC443107.1|FC443107
EST:     TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAG                         GAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
genomic: TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAGgtacagtgga ... tattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
EST: gi|37838817|gb|BJ596825.1|BJ596825
EST:     TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAG                         GAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
genomic: TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAGgtacagtgga ... tattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
EST: gi|208369491|gb|DC955904.1|DC955904
EST:     TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAG                         GAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT
genomic: TAGCGACGTTCCTAGATTCAGCAAAGTCCTTCAACATAATCTATGCCAAGgtacagtgga ... tattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacagcacttggctcctcattgtggttgttgtgattgtatgatgtattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTTGGACCTGCTGCAAATCGATTGCTGGATTCTTATAGCCAATTGCTTAAG
 cccttac  putative branch site (score: 3)
                                  attgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtggaagcgtgatgcagttctccaataaatcttgagatttggtccattgtattagcgcagctgtaagcacggagggttcatgcacggccattcccttacagcacttggctcctcattgtggttgttgtgattgtatgatgtattgagcagGAAATTCGGCCATGGACGCATATGATGGACGTTCCCCAGCTTCATGGACTTGGACCTGCTGCAAATCGATTGCTGGATTCTTATAGCCAATTGCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA