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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaaaagaaaatatctttcgagcatgactttgcatgttcgcattgttttcttaattggtttttcgtgtgagtggagaaacgctagcgtttttttttctcttaaattaatggttttttgttttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGACTCGGAGCAAGCAATTGGAGCTGGAACTATTGGTTCTTCCGAGGCGATAA

Basic information

species Selaginella moellendorffii
transcript EFJ18071
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|70669350|gb|DN837927.1|DN837927
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169025137|gb|FE433892.1|FE433892
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169031371|gb|FE441187.1|FE441187
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169050085|gb|FE460153.1|FE460153
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169042692|gb|FE451511.1|FE451511
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169019233|gb|FE428146.1|FE428146
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169063238|gb|FE472696.1|FE472696
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169105456|gb|FE504062.1|FE504062
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169105455|gb|FE504061.1|FE504061
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169108572|gb|FE510787.1|FE510787
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169040842|gb|FE447893.1|FE447893
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169072350|gb|FE480249.1|FE480249
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169096776|gb|FE499792.1|FE499792
EST:     AGAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCGGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169030667|gb|FE439573.1|FE439573
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGNGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169034082|gb|FE442803.1|FE442803
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169027576|gb|FE432750.1|FE432750
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169103423|gb|FE508895.1|FE508895
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169045970|gb|FE451241.1|FE451241
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
EST: gi|169075987|gb|FE482854.1|FE482854
EST:     ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAG                         GATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC
genomic: ACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGAC

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: 58

CACCACTTGGATGGAGCCCGAGTGTGATAAGCTCGTCATGGCCTCGCTCAACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaag ... ttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGACTCGGAGCAAGCAATTGGAGCTGGAACTATTGGTTCTTCCGAGGCGATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacgctagcgtttttttttctcttaaattaatggttttttgttttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGACTCGGAGCAAGCAATTGGAGCTGGAACTATTGGTTCTTCCGAGGCGATAA
                           aattaat  putative branch site (score: 58)
                                    ttttttgttttgctc  putative PPT
            tttttttttctcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgaaaagaaaatatctttcgagcatgactttgcatgttcgcattgttttcttaattggtttttcgtgtgagtggagaaacgctagcgtttttttttctcttaaattaatggttttttgttttgctcgtagGATCGATGCGTGAACATGATCGCTCGGCTGTTCAATGCTCCAGTGGGAGACTCGGAGCAAGCAATTGGAGCTGGAACTATTGGTTCTTCCGAGGCGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA