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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagtcttatgcataatatacttgtcatctccatcaatttttggtaacatacacataccttttgctgtctcaaacgagcgataattgtgtttttatcagGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACCAATCGAGCTGATGTTTTGGATCCTGCTCTTAGGCGACCTGGACGATTTG

Basic information

species Physcomitrella patens
transcript PP1S10_296V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 6
-----tgtagtcttatgcataatatacttgtcatctccatcaatttttggtaacatacacataccttttgctgt--ctcaaacgagcgataattgtgtt---tttatc-----------agGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACCAATCGAGCTGATGTTTTGGATCCTGCTCTTAGGCGACCTGGACGATTTG
       ||||     |     ||  ||||| ||    |  |  ||||  | ||||||||| | |||| | ||     |||  ||   ||  | |||||   ||| ||           ||||  ||||||||||||| | || |||| |||| ||||||||||| || || || ||||| |||||||| |||||||| ||  | || |||||  ||||||
gtattgatagtaaagagtcctttaatcttgtgattctgactatattttactcacatacacacatctttagttggggtccaattgaattatcttcgtgttaattttctctgaatctacctagGAAATGGATGGATTTGACACCAACTCAGCTGTCATTGTACTTGGAGCAACAAACCGAGCAGATGTTTTAGATCCTGCCCTCCGACGCCCTGGGAGATTTG

upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G163193_T02 (Zea mays), 3'ss of exon 6
tgtagtcttatgcataatatacttgtcatctccatcaatttttggtaa---catacacataccttttgctgtctcaaacgagcgataattgtgtttttatc-agGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACCAATCGAGCTGATGTTTTGGATCCTGCTCTTAGGCGACCTGGACGATTTG
  ||    ||   ||| |    || ||||    ||   ||||  | ||      | |      | ||  ||  | |   |    |   ||| ||||||  | ||||  ||||||| || || | ||  ||  |||| |||||||| ||||| || |||||||||||||||||||||||||| ||||||||||||||  ||||||
-ttaac--taaaaatactgc-tttatcatgcaaattttttttgagaaagggtggaaatggtattattattggtttagctgccttaattttgggtttttccccagGAAATGGATGGCTTCGACACCAATTCGGCTGTCATTGTACTAGGGGCAACAAATCGAGCTGATGTTTTGGATCCTGCCCTTAGGCGACCTGGGAGATTTG

upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 6
tgtagtcttatgcataatatacttgtcat-ctccatcaatttttggtaacatacacatac----cttttgctgtctcaaacgagcgataattgtgtttttatcagGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACCAATCGAGCTGATGTTTTGGATCCTGCTCTTAGGCGACCTGGACGATTTG
     |  || | ||| |    || |||| |   ||   ||||||  ||    |  | |      | ||  ||  | |   |        ||| ||| |   |||||  ||||||| ||||| | || |||  |||| |||||| | ||||| || |||||||||||||||||||||||||| |||||||| |||||  ||||||
----ctactaaggatactgc-tttatcatgcaatatttgtttttgagaaagggcggaaatggtattattattggtttagctgccttgattttgggttctccccagGAAATGGATGGCTTTGATACCAACTCGGCTGTCATTGTATTGGGGGCAACAAATCGAGCTGATGTTTTGGATCCTGCCCTTAGGCGCCCTGGGAGATTTG

upper sequence: PP1S10_296V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
tgtagtcttatgcataatatacttgtcatctccatcaatttttggtaacatacacataccttttgctgtctcaaacgagcgataattgtgtttttatcagGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACCAATCGAGCTGATGTTTTGGATCCTGCTCTTAGGCGACCTGGACGATTTG
 |||   || |  || ||  |||| || |  |        |||  | |  |   |||      |      | | | |   |  || || ||||    |||||| ||||||| ||||| || |||||  | |||||||| ||||| |||||||||||||||||||| || || ||||| ||  | || |||||  ||||||
-gtaagtttgta-attatgcacttttcctgccagagttgctttcttgatctttgcat------tatccatttatatgt-tgggaactg-gttta---cagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG

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|162254897|gb|FC431082.1|FC431082
EST:     GAAGTGTTGGGAATGATGAGCGAGAGCAAACCCTCAACCAGCTTCTCACA                         GAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACC
genomic: GAAGTGTTGGGAATGATGAGCGAGAGCAAACCCTCAACCAGCTTCTCACAgtaagtattt ... tttttatcagGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACC
EST: gi|100401189|gb|BY990875.1|BY990875
EST:     GAAGTGTTGGGAATGATGAGCGAGAGCAAACCCTCAACCAGCTTCTCACA                         GAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACC
genomic: GAAGTGTTGGGAATGATGAGCGAGAGCAAACCCTCAACCAGCTTCTCACAgtaagtattt ... tttttatcagGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacatacacataccttttgctgtctcaaacgagcgataattgtgtttttatcagGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACCAATCGAGCTGATGTTTTGGATCCTGCTCTTAGGCGACCTGGACGATTTG
 tggtaac  putative branch site (score: 2)
                                             tttttatc  putative PPT
                                    ataattgtgtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagtcttatgcataatatacttgtcatctccatcaatttttggtaacatacacataccttttgctgtctcaaacgagcgataattgtgtttttatcagGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACCAATCGAGCTGATGTTTTGGATCCTGCTCTTAGGCGACCTGGACGATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT