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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgagatgctttcttacaatgcaacttaaaattcaagtggcttttggactttgtgcatatggccgacacaattatactaagttttctttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTTTTTGATTCAGTGTTAACCGGGAAGAACTTAATGGGCATGTTCATGGCAA

Basic information

species Physcomitrella patens
transcript PP1S15_388V6.3
intron # 6
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|37825662|gb|BJ583728.1|BJ583728
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|67699821|gb|BJ960054.1|BJ960054
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|162262230|gb|FC437141.1|FC437141
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|162244248|gb|FC420978.1|FC420978
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|37839052|gb|BJ597060.1|BJ597060
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|37850347|gb|BJ608355.1|BJ608355
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTAC-TTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|67693024|gb|BJ953257.1|BJ953257
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|37823729|gb|BJ581795.1|BJ581795
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|208366176|gb|DC955277.1|DC955277
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|162214631|gb|FC390662.1|FC390662
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|67569756|gb|BJ942580.1|BJ942580
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|162228570|gb|FC405286.1|FC405286
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|18335982|gb|BJ168003.1|BJ168003
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGCGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|37843863|gb|BJ601871.1|BJ601871
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
EST: gi|19788745|gb|BQ040893.1|BQ040893
EST:     ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAG                         GTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT
genomic: ACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTT

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: 28 (upstream exon), 17 (downstream exon)
Score: 6

ATGTTTATATTGCTCTCATGCGTTCTTGCTGTATTCTGCAACATCAGCCAGTATTTGTGTATCGGGAGATTCTCTGCAGTCACATTCCAGgttatctaat ... ttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTTTTTGATTCAGTGTTAACCGGGAAGAACTTAATGGGCATGTTCATGGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggactttgtgcatatggccgacacaattatactaagttttctttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTTTTTGATTCAGTGTTAACCGGGAAGAACTTAATGGGCATGTTCATGGCAA
                                       ttttctttctttgt  CT-rich tract
                           aattatactaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgagatgctttcttacaatgcaacttaaaattcaagtggcttttggactttgtgcatatggccgacacaattatactaagttttctttctttgtagGTTCTGGGACACATGAAGACTGTTTGCGTCCTACTTTTGGGATGGATTCTTTTTGATTCAGTGTTAACCGGGAAGAACTTAATGGGCATGTTCATGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC