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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgctattttgctgattttctgatctgtcttgttcaagctgttcctgtatgattgttttttacttgtagcccatcatttaattttcgacgttggcg...

Basic information

species Physcomitrella patens
transcript PP1S97_259V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv11s0016g02690.t01 (Vitis vinifera), 5'ss of exon 3
TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGT-AGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgctattttgctgattttctgatctgtcttgttcaagctgttcctgtatgattgttttttacttgtagcccatcatttaattttcgacgttggcg
| || || ||||| ||||||||||| |||||||| |||||||||| || | ||  |      || || |      ||   | |   || |  |||  ||| |   |    | |    ||||||    | |  ||    | |||  |||| ||                             
TCGTGGGCTTCGGGAAGAAGAGGGGACCCAACTCGTCGGAGAAgtgagcgcaaaata-----tgaaaatttgaagactggttttgttgtt--tttaatgaatggttaggatat----ttcaagtc--tacaatactggtttttgatactggtgtta-------------------------
















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|162274218|gb|FC449978.1|FC449978
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|162278104|gb|FC453923.1|FC453923
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|162235480|gb|FC411615.1|FC411615
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|67692486|gb|BJ952719.1|BJ952719
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|162216409|gb|FC393242.1|FC393242
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|18343785|gb|BJ175823.1|BJ175823
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|67699773|gb|BJ960006.1|BJ960006
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|18335631|gb|BJ167651.1|BJ167651
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|162227643|gb|FC402324.1|FC402324
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|162207654|gb|FC383531.1|FC383531
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|18347831|gb|BJ179878.1|BJ179878
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|162278103|gb|FC453922.1|FC453922
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|18327360|gb|BJ159362.1|BJ159362
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|18351472|gb|BJ183524.1|BJ183524
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|37830817|gb|BJ588829.1|BJ588829
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|37822977|gb|BJ581043.1|BJ581043
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|67569232|gb|BJ942056.1|BJ942056
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|37826921|gb|BJ584933.1|BJ584933
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
EST: gi|67576266|gb|BJ949090.1|BJ949090
EST:     ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT                         AGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT
genomic: ACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTT

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: 66

TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgcta ... gaaagtgcagAGAGTCGGGGAGCCTGGTGATAACCCTAGCAACATGTTACTTCTTGGCGTTAGCAGCATTAAGTGATTGAACATGTAATTACCTGGCTATAACTGCCACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCATgtaagtgctattttgctgattttctgatctgtcttgttcaagctgttcctgtatgattgttttttacttgtagcccatcatttaattttcgacgttggcg

- - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA