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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagagataccctgtcgtcgcttattaaagataatttgatgactcttacaccattcgttaaccttccttaccgcctatggtttgctgcataatggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTGGTTGCCTCAAGCAAGGCAAGATTCCACAACAGCAGATGAG

Basic information

species Physcomitrella patens
transcript PP1S62_89V6.3
intron # 6
splice site 3'
intron type U2

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|18338070|gb|BJ170094.1|BJ170094
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
EST: gi|208393768|gb|DC928660.1|DC928660
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
EST: gi|162253104|gb|FC428936.1|FC428936
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
EST: gi|100404747|gb|BY991263.1|BY991263
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTC-TTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTC
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTC
EST: gi|162183078|gb|FC360644.1|FC360644
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
EST: gi|208367645|gb|DC955004.1|DC955004
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
EST: gi|208393509|gb|DC949671.1|DC949671
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
EST: gi|162183077|gb|FC360643.1|FC360643
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
EST: gi|208392795|gb|DC953692.1|DC953692
EST:     GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGG                         GAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG
genomic: GGCAGTGGTGGCACAGCTCCATCGTCACTTCCTTCCTTTCCTATGCCCGGgtaaggttgc ... atggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaccattcgttaaccttccttaccgcctatggtttgctgcataatggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTGGTTGCCTCAAGCAAGGCAAGATTCCACAACAGCAGATGAG
                  tccttac  putative branch site (score: 2)
                                          ataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagagataccctgtcgtcgcttattaaagataatttgatgactcttacaccattcgttaaccttccttaccgcctatggtttgctgcataatggctgtagGAGCAACAGCGTTTCTTCTTTTCGGGCGGTGATGAACAGAATACAAGGCTGGTTGCCTCAAGCAAGGCAAGATTCCACAACAGCAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgca