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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttttcttccttgttgtatcatcagttttctttgtttgagattcgacactgaccaaagttcgctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCTGCCGAGCAAAACTTCGTCCGCAAGCATGTGCTGGAGCAGGCCAAGAGCC

Basic information

species Selaginella moellendorffii
transcript EFJ32730
intron # 3
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|169031601|gb|FE439066.1|FE439066
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169108520|gb|FE510774.1|FE510774
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169061202|gb|FE469093.1|FE469093
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169054017|gb|FE461316.1|FE461316
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169033697|gb|FE441625.1|FE441625
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169077399|gb|FE485896.1|FE485896
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169094670|gb|FE494563.1|FE494563
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169113267|gb|FE515218.1|FE515218
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGGTCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169112432|gb|FE510148.1|FE510148
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169045794|gb|FE453067.1|FE453067
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169111087|gb|FE513717.1|FE513717
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169032593|gb|FE437724.1|FE437724
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169056611|gb|FE463849.1|FE463849
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169058318|gb|FE466046.1|FE466046
EST:     CGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATNCA-CCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCC
genomic: CGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCAT-CAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCC
EST: gi|169114169|gb|FE515704.1|FE515704
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169061943|gb|FE470237.1|FE470237
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATG
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATG
EST: gi|169021575|gb|FE428610.1|FE428610
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGT
EST: gi|169102674|gb|FE504467.1|FE504467
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169034582|gb|FE444603.1|FE444603
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGA
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGA
EST: gi|169040718|gb|FE447353.1|FE447353
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169032129|gb|FE438762.1|FE438762
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169088279|gb|FE491997.1|FE491997
EST:     CGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATNCA-CCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCC
genomic: CGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCAT-CAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCC
EST: gi|169032268|gb|FE439330.1|FE439330
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169100709|gb|FE502169.1|FE502169
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169074358|gb|FE484267.1|FE484267
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169049678|gb|FE458797.1|FE458797
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169064968|gb|FE475040.1|FE475040
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
EST: gi|169047697|gb|FE454865.1|FE454865
EST:     ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAG                         ATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT
genomic: ACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCT

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: 54

TAACAAGATCGAGCCTGTGTCGCTGGAGGAGCTAGGGAGGCCAAGGATCGACGTCGTGGTGAATTGCTCCGGGGTGTTTAGAGACTTGTTCATCAACCAGgtcagttttc ... gctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCTGCCGAGCAAAACTTCGTCCGCAAGCATGTGCTGGAGCAGGCCAAGAGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatcagttttctttgtttgagattcgacactgaccaaagttcgctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCTGCCGAGCAAAACTTCGTCCGCAAGCATGTGCTGGAGCAGGCCAAGAGCC
                              cactgac  putative branch site (score: 54)
                                          ttcgctc  putative PPT
         ttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttttcttccttgttgtatcatcagttttctttgtttgagattcgacactgaccaaagttcgctcgtgtagATGAATTTGCTCGATCGAGCAGTGAAGATGGTCGCAGAGCTGGACGAGCCTGCCGAGCAAAACTTCGTCCGCAAGCATGTGCTGGAGCAGGCCAAGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG