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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcgattaggcgatttagggtttggcatttgacatttgtatctgaagtagtttgcaaagggagattcgaaaattgaatttgttttgtttcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAGCTTGGACAGTAGATGGAGTTGACCTCCCTTAGTGTAATCACATATACGC

Basic information

species Physcomitrella patens
transcript PP1S372_10V6.1
intron # 2
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|162232484|gb|FC408359.1|FC408359
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162209539|gb|FC385635.1|FC385635
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162251424|gb|FC425544.1|FC425544
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|67694588|gb|BJ954821.1|BJ954821
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162227865|gb|FC403673.1|FC403673
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162223439|gb|FC400629.1|FC400629
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162217587|gb|FC393991.1|FC393991
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162220057|gb|FC397028.1|FC397028
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|19782337|gb|BQ039841.1|BQ039841
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|18343942|gb|BJ175981.1|BJ175981
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|37837393|gb|BJ595401.1|BJ595401
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|18354317|gb|BJ186373.1|BJ186373
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162230732|gb|FC406363.1|FC406363
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162217586|gb|FC393990.1|FC393990
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162209538|gb|FC385634.1|FC385634
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162224880|gb|FC401088.1|FC401088
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|37835788|gb|BJ593800.1|BJ593800
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162226817|gb|FC403837.1|FC403837
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|18358029|gb|BJ190088.1|BJ190088
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|67571269|gb|BJ944093.1|BJ944093
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|67696810|gb|BJ957043.1|BJ957043
EST:     GGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: GGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|67698725|gb|BJ958958.1|BJ958958
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|67575264|gb|BJ948088.1|BJ948088
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162241160|gb|FC414165.1|FC414165
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162217613|gb|FC394017.1|FC394017
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|162218209|gb|FC394201.1|FC394201
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
EST: gi|37823133|gb|BJ581199.1|BJ581199
EST:     ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAG                         GGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG
genomic: ACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 63

TGTTGCCTCAGTTCAGCTCAATGTGGGTCATGTTGACGAAAATGGTGTCTACACCGGGCAGTTCACCACCTTCGCCCTATGCGGGTTTGTTCGTGCTCAGgtgggtatac ... tcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAGCTTGGACAGTAGATGGAGTTGACCTCCCTTAGTGTAATCACATATACGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtagtttgcaaagggagattcgaaaattgaatttgttttgtttcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAGCTTGGACAGTAGATGGAGTTGACCTCCCTTAGTGTAATCACATATACGC
                                  tttgttttgtttctt  CT-rich tract
                         aaaattgaatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttcgattaggcgatttagggtttggcatttgacatttgtatctgaagtagtttgcaaagggagattcgaaaattgaatttgttttgtttcttgtgcagGGTGATGCCGACAGTGCCTTGGATAGATTGTGGGCGAAGAAGAAGGCCGAGCTTGGACAGTAGATGGAGTTGACCTCCCTTAGTGTAATCACATATACGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA