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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcgacgtgaccgaattgatggtcacctggaattagacatgcttatggattagtatgtgtgcattatgtcattaacaacatacattttttttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCTGAGATTGCCAAGAACCTGCGCAAGTACAGCAAGAAGTACGAGGCTGACG

Basic information

species Physcomitrella patens
transcript PP1S130_248V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S130_248V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 10
-tttcgacgtgaccgaattgatggtcacctggaattagacatgcttatggattagtatgtgtgcattatgtcattaacaacatacattttttttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCTGAGATTGCCAAGAACCTGCGCAAGTACAGCAAGAAGTACGAGGCTGACG
 | | || ||   | |    |   |   ||||| |   |  | || || | ||   |    || | |   |  | |   || |  ||||  |   |  |||||  |||||||||| ||||| ||  | || || || || ||  | || |  |||||||| ||||||||| | |||||||||||||||||||||   || |
gtatggaggt--tccatcctacccttttctggactctcatgt-ctcattgctttacaccattgtaatcctttgtcatttactttaatttactggta--cagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG
















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|162255418|gb|FC431832.1|FC431832
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|162195248|gb|FC370821.1|FC370821
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|208350283|gb|DC925745.1|DC925745
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|37850644|gb|BJ608652.1|BJ608652
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|208363001|gb|DC946898.1|DC946898
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|37824076|gb|BJ582142.1|BJ582142
EST:     GGGACAGGTTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGC
genomic: GGGACAGG-TTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGC
EST: gi|162169045|gb|FC345727.1|FC345727
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|162255419|gb|FC431833.1|FC431833
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|162265641|gb|FC441097.1|FC441097
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|162156616|gb|FC333264.1|FC333264
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|162169044|gb|FC345726.1|FC345726
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
EST: gi|162160006|gb|FC335668.1|FC335668
EST:     CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAG                         TTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT
genomic: CATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGGTTTTTCCAGgtacgtgtac ... tttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggattagtatgtgtgcattatgtcattaacaacatacattttttttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCTGAGATTGCCAAGAACCTGCGCAAGTACAGCAAGAAGTACGAGGCTGACG
                         cattaac  putative branch site (score: 2)
                                      cattttttttc  putative PPT
                          attaacaacatacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcgacgtgaccgaattgatggtcacctggaattagacatgcttatggattagtatgtgtgcattatgtcattaacaacatacattttttttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCTGAGATTGCCAAGAACCTGCGCAAGTACAGCAAGAAGTACGAGGCTGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT