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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattgcttccgtgagtgatctatggcatgaaacgtctcagatctttggttttttcgtatgaactttgactaatgacatttttctgccattggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCAGGCGACACCCGTGCTCAGGAGGTCGTCGGCATGCTGAAGACCAACGACC

Basic information

species Physcomitrella patens
transcript PP1S78_205V6.1
intron # 1
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|162241869|gb|FC418124.1|FC418124
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|18333160|gb|BJ165174.1|BJ165174
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162218872|gb|FC394415.1|FC394415
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162267047|gb|FC443083.1|FC443083
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTTTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|15728310|gb|BI740723.1|BI740723
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162273839|gb|FC449770.1|FC449770
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162267048|gb|FC443084.1|FC443084
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|19783476|gb|BQ040019.1|BQ040019
EST:     CCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162205829|gb|FC381067.1|FC381067
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|19789694|gb|BQ041455.1|BQ041455
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162273838|gb|FC449769.1|FC449769
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162264596|gb|FC440892.1|FC440892
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|18325204|gb|BJ157200.1|BJ157200
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162205857|gb|FC381095.1|FC381095
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162241870|gb|FC418125.1|FC418125
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
EST: gi|162226058|gb|FC401024.1|FC401024
EST:     CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAAT                         GTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA
genomic: CCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCA

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: 34 (upstream exon), 35 (downstream exon)
Score: 21

GGTCACCTGCGAGGCGAACACCGCCTTGACGATCACTTTGAGCACCGGCGCCCTGCTGTTCCTCGGCCGCTTCGTCTTCCTCCCCTTCCAGAGAGATAATgtgcgtcaca ... tggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCAGGCGACACCCGTGCTCAGGAGGTCGTCGGCATGCTGAAGACCAACGACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttttttcgtatgaactttgactaatgacatttttctgccattggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCAGGCGACACCCGTGCTCAGGAGGTCGTCGGCATGCTGAAGACCAACGACC
                      gactaat  putative branch site (score: 21)
                              acattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattgcttccgtgagtgatctatggcatgaaacgtctcagatctttggttttttcgtatgaactttgactaatgacatttttctgccattggattttagGTGTCGAGGCAGGGCTTACCAGAGCAGAATGGAGTGACCCACTACGACGCAGGCGACACCCGTGCTCAGGAGGTCGTCGGCATGCTGAAGACCAACGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA