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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaaagtattgattgaatgctttgaaaatgatttgaaagcctccttctctgggcattcctattgtttcatcgagccatggtttgtattcccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA

Basic information

species Physcomitrella patens
transcript PP1S4_73V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 2
-tttgaaagtattgattgaatgctttgaaaatgatttgaaagcctcctt-ctctgggcattcctattgtttcatcgagccatggtttgtattcc-cttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA
 |||     |   || |      | |     || |||      |||  |  | ||    |  |  || || |  |     ||  | | ||| || || | |||||||| |||||||||||||| || || ||||||||||| |||||||| |||||||| || ||||| ||||| |||||  | || || ||||| || ||||
gtttccctctcaagactct-cattctcgtggtgttttttttttctctgtgttttgattgtgacccttcttgctgctgataataatgtttatgccactctgcagGTTCCTTTCTGCCCAATGGTTGGTTCTGAAGTTTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTA

upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 2
tttgaaagtattgattgaatgctttgaaaatgatttgaaagcctccttctctgggcatt-cctattgtttcatcgagccatggtttgtattcc-cttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA
                   | ||||   || || |   |  | |  |  | ||    || ||  || || |  |     ||    | |||||| || | ||||| || |||||||| ||||| || |||||||||||||| || ||||| |||||||| || ||||| ||||| ||||| || || || ||||| || ||||
-----------------gtttctttctcaa-gactctcattctttgtgttgtgattgttaccccttcttgctgcttataattaagtttattccactctgcagGTACCGTTCTGCCCTATGGTTGGCTCCGAAGTTTACTCCTCGGAAGTAAAGAAGACTGAGGTTCTCATGGAAAATTTTCGACGGGCCATTGGTCTGCGTA

upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
-----tttgaaagtattgattgaa---tgctttg--aaaatgatttgaaa--gcctccttctctgggcattcctattgtttcatcgagcca--------tggtttgtattcccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA
     |||| | || |   ||      | |||||  | | || ||  | |  || || || | ||    ||  |  | || | |  |||          ||| |||| |     || |||||||||||||| |||||||| || || || |||||||||||||| |||||||| || || ||||| |||||||||||  | ||||| ||||| || ||||
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA

upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 2
tttgaaagtattgattgaatgctttgaaaatgatttgaaagcctccttctctgggcattcctattgtttcatcgagccatggtttgtattcccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA
                              |  ||| ||   |   |  |||   | ||||| |  |   || |        |||||  |    || ||||||||||| || |||||||| || || || |||| ||| || |||||||||||||| |||||||| ||||| || || || ||  | || || || ||||
----------------------------gtttgtttcaagctcatttcttct---ctttcct-tcatacaatggga----attttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA

upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 2
tttgaaagtattgattgaatgctttgaaaatgatttgaaagcctccttctctgggcattcctattgtttcatcgagccatggtttgtattcccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA
                              |  ||| ||   |   |  |||   | ||||| |  |   || |        |||||  |    || ||||||||||| || |||||||| || || || |||| ||| || |||||||||||||| |||||||| ||||| || || || ||  | || || || ||||
----------------------------gtttgtttcaagctcatttcttct---ctttcct-tcatacaatgggatt----tttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA

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|162250404|gb|FC426266.1|FC426266
EST:     CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAG                         GTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
genomic: CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAGgtaacggcaa ... cccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
EST: gi|18355135|gb|BJ187194.1|BJ187194
EST:     CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAG                         GTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
genomic: CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAGgtaacggcaa ... cccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
EST: gi|162237933|gb|FC412534.1|FC412534
EST:     CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAG                         GTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
genomic: CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAGgtaacggcaa ... cccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
EST: gi|100363873|gb|BY966213.1|BY966213
EST:     CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAG                         GTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
genomic: CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAGgtaacggcaa ... cccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
EST: gi|162252178|gb|FC425856.1|FC425856
EST:     CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAG                         GTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
genomic: CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAGgtaacggcaa ... cccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
EST: gi|67717889|gb|BJ968148.1|BJ968148
EST:     CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAG                         GTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
genomic: CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAGgtaacggcaa ... cccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
EST: gi|67719827|gb|BJ970086.1|BJ970086
EST:     CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAG                         GTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG
genomic: CGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAGgtaacggcaa ... cccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctctgggcattcctattgtttcatcgagccatggtttgtattcccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA
                                     tttgtattcccttttc  CT-rich tract
                tattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgaaagtattgattgaatgctttgaaaatgatttgaaagcctccttctctgggcattcctattgtttcatcgagccatggtttgtattcccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA