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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATCCGGAACATCGATTTGGTGTATGGTGGAGGTAGTATTGGGCTGATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcatgcccctgaaacttggccgatcatgttaatcgtgtccaactgatgccgcttcgtgatcacaagtttttgaaagtgtggtcttttggtcgta...

Basic information

species Physcomitrella patens
transcript PP1S13_423V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S13_423V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA04G05550.2 (Glycine max), 5'ss of exon 1
--GTGATCCGGAACATCGATTTGGTGTATGGTGGAGGTAGTATTGGGCTGATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcatgccc-----ctgaaacttggccgatcatgttaatcgt----gtccaactgatgccgcttcgtgatcacaagtttttgaaagtgtggtctt-ttggtcgta---
|| | ||||||| || |||||||||||||| || ||| ||||||||||||| | | | |||| ||| | | ||||||| || | || ||||| ||||| | |||| || | ||||||| | | || | | | | || | || || | | | | || | ||||
AGGTTAAGAGGAACATAGACTTGGTGTATGGTGGGGGCAGTGTTGGGCTGATGGGCTTAATATCTCAGAGAGTGTATGATGGAGGCTGCCATGTCCTAGGgtatgtgcaaacagaaaaaaagaaaattactttttagtgttaatgataattgatcacattgtctcaccgtttgtttgtttcttctttacattttaccctcactctacgtacag

upper sequence: PP1S13_423V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA14G11070.1 (Glycine max), 5'ss of exon 1
GTGATCCGGAACATCGATTTGGTGTATGGTGGAGGTAGTATTGGGCTGATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcatgcccctgaaacttggccgatcatgttaatcgtgtccaactgatgccgcttcgtgatcacaagtttttgaaagtgtggtcttttggtcgta
|| | ||||||| || |||||||||||||| || ||| ||||||||||||| | | | | |||| | | | | ||||||| || | || ||||| | ||| |||| | || | |||| || || | | | || | | ||| |||| |
GTTAAGAGGAACATTGACTTGGTGTATGGTGGGGGAAGTGTTGGGCTGATGGGCCTAATATCCCAGAGAATGTATGATGGAGGCTGCCATGTTCTAGGgtatg--------cctaaaacaacattctgtgtattg-tagtgtttaattgtcatggatactctatatctgttcttttgctgtgtag-------------

upper sequence: PP1S13_423V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA17G34510.1 (Glycine max), 5'ss of exon 2
GTGATCCGGAACATCGATTTGGTGTATGGTGGAGGTAGTATTGGGCTGATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGC--------AAAGTATGTGGgtaagtgcatgcccc------tgaaacttggccgatcatgttaatcgtgtccaactgatgccgcttcgtgatcacaagtttttgaaagtgtggtcttttggtcgta----------------------------------------------------------
|| | ||||||| || |||||||||||||| || ||| ||||||||||||| | | | | |||| | | | | ||||||| || | ||||| | || ||||| || |||||| | | | || | | ||| | ||| || || | || ||| ||| |
GTTAAGAGGAACATTGACTTGGTGTATGGTGGGGGAAGTGTTGGGCTGATGGGCCTAATATCCCAGAGAATGTATGATGGAGGCTGCCATGTTCTAGGgtatgcctgaaacaacatgctttgtattgcagtgtttaatttatcatggatactctata-gtctattctttcactgtgtaggcttgttgttattggtttaatcattttgtctcaccctttgtttgttgtctatttgccttttcttgtatttttctcctctctacatatacag

upper sequence: PP1S13_423V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA04G05550.1 (Glycine max), 5'ss of exon 2
GTGATCCGGAACATCGATTTGGTGTATGGTGGAGGTAGTATTGGGCTGATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcatgcccc-----tgaaacttggccgatcatgttaatcgt----gtccaactgatgccgcttcgtgatcacaagtttttgaaagtgtggtctt-ttggtcgta---
|| | ||||||| || |||||||||||||| || ||| ||||||||||||| | | | |||| ||| | | ||||||| || | || ||||| ||||| | |||| || | ||||||| | | || | | | | || | || || | | | | || | ||||
GTTAAGAGGAACATAGACTTGGTGTATGGTGGGGGCAGTGTTGGGCTGATGGGCTTAATATCTCAGAGAGTGTATGATGGAGGCTGCCATGTCCTAGGgtatgtgcaaacagaaaaaaagaaaattactttttagtgttaatgataattgatcacattgtctcaccgtttgtttgtttcttctttacattttaccctcactctacgtacag

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|100450410|gb|CJ974249.1|CJ974249
EST:     ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGG                         CGTTATTCCAAAGGCATTGATTGGAAAANAACTTACTGGAAGCACAGTGGG
genomic: ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcat ... gtgaaaccagCGTTATTCCAAAGGCATTGATTGGAAAAGAACTTACTGGAAGCACAGTGGG
EST: gi|18352037|gb|BJ184090.1|BJ184090
EST:     ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGG                         CGTTATTCCAAAGGCATTGATTG
genomic: ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcat ... gtgaaaccagCGTTATTCCAAAGGCATTGATTG
EST: gi|208376681|gb|DC932145.1|DC932145
EST:     ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGG                         CGTTATTCCAAAGGCATTGATTGGAAAAGAACTTACTGGAAGCACAGTGGG
genomic: ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcat ... gtgaaaccagCGTTATTCCAAAGGCATTGATTGGAAAAGAACTTACTGGAAGCACAGTGGG
EST: gi|208360660|gb|DC930471.1|DC930471
EST:     ATGGGTCAAGTGGCACAGACAGTCNAAGCTGGAGGCGNCAAAGTATGNGG                         CGTTATTCCAAAGGCATTGATTGGAAAANAACTTACTGGAAGCACAGTGAG
genomic: ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcat ... gtgaaaccagCGTTATTCCAAAGGCATTGATTGGAAAAGAACTTACTGGAAGCACAGTGGG
EST: gi|208400182|gb|DC904830.1|DC904830
EST:     ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGG                         CGTTATTCCAAAGGCATTGATTGGAAAAGAACTTACTGGAAGCACAGTGGG
genomic: ATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcat ... gtgaaaccagCGTTATTCCAAAGGCATTGATTGGAAAAGAACTTACTGGAAGCACAGTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATCCGGAACATCGATTTGGTGTATGGTGGAGGTAGTATTGGGCTGATGGGTCAAGTGGCACAGACAGTCGAAGCTGGAGGCGGCAAAGTATGTGGgtaagtgcatgcccctgaaacttggccgatcatgttaatcgtgtccaactgatgccgcttcgtgatcacaagtttttgaaagtgtggtcttttggtcgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG