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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttctctcgttttcacattgttcttttcttaatttcaatgtcgacagcattatatgcttcctgatttctaacgtccggttattttctttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTGGGATAAGAAGCTACTGTCAGGTGCAGTAGTTGTTCCAGAAATCGGAAAA

Basic information

species Physcomitrella patens
transcript PP1S61_112V6.1
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|208376453|gb|DC902750.1|DC902750
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCANATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|162153960|gb|FC329467.1|FC329467
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|162224737|gb|FC400737.1|FC400737
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|100376203|gb|BY986072.1|BY986072
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|18332323|gb|BJ164336.1|BJ164336
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACC
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACC
EST: gi|208371195|gb|DC931613.1|DC931613
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|208385210|gb|DC911414.1|DC911414
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|162245923|gb|FC420811.1|FC420811
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|100449571|gb|CJ973826.1|CJ973826
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|100436177|gb|BY979418.1|BY979418
EST:     CCACGGTTATCAAAAACTCCGGGAATGGATCCCGAGAGTGAAAATGACAG                         GCGGTTTACTGGGCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTG-TG
genomic: CCACGGTTATCAAAAACTCCGG-AATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|100415960|gb|BY957009.1|BY957009
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|100449948|gb|CJ974017.1|CJ974017
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|162191379|gb|FC368162.1|FC368162
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
EST: gi|67571782|gb|BJ944606.1|BJ944606
EST:     TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAG                         GCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG
genomic: TCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTG

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), 34 (downstream exon)
Score: 8

TGCCGAAACTTTCTGTGAGTATCAAGAAGGCTGCAAGTGGACGTAGCAGTTCCACGGTTATCAAAAACTCCGGAATGGATCCCGAGAGTGAAATTGACAGgttttctctc ... tttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTGGGATAAGAAGCTACTGTCAGGTGCAGTAGTTGTTCCAGAAATCGGAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacagcattatatgcttcctgatttctaacgtccggttattttctttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTGGGATAAGAAGCTACTGTCAGGTGCAGTAGTTGTTCCAGAAATCGGAAAA
                        ttctaac  putative branch site (score: 8)
                                tccggttattttcttt  CT-rich tract
                                     ttattttctttttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttctctcgttttcacattgttcttttcttaatttcaatgtcgacagcattatatgcttcctgatttctaacgtccggttattttctttttttcagGCGGTTTACTGGCCGAGTGTTGGCACCAGCTCCTGGAGACTCAGATTGGTGGGATAAGAAGCTACTGTCAGGTGCAGTAGTTGTTCCAGAAATCGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC