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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatttttacaaggtcaaccgttgtggttgaactgcctgtagctgtaatttgctaggtgagggatgctgttaagctgtgccgggttagtatcaggtgatctgtcaggtgatcgtctcaaactttaaagaaaaaaattcttgtactttctgaacagttttgatccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG

Basic information

species Physcomitrella patens
transcript PP1S2_16V6.1
intron # 4
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|67716905|gb|BJ967164.1|BJ967164
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208391390|gb|DC933567.1|DC933567
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208389935|gb|DC937766.1|DC937766
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208376484|gb|DC922515.1|DC922515
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|162236728|gb|FC413407.1|FC413407
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|67719943|gb|BJ970202.1|BJ970202
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|18361523|gb|BJ193589.1|BJ193589
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|162192347|gb|FC371642.1|FC371642
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208382233|gb|DC914852.1|DC914852
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|162279719|gb|FC455627.1|FC455627
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|67728248|gb|BJ978507.1|BJ978507
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|162279720|gb|FC455628.1|FC455628
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208368148|gb|DC947708.1|DC947708
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|18365612|gb|BJ197689.1|BJ197689
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|162194794|gb|FC371641.1|FC371641
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|67695781|gb|BJ956014.1|BJ956014
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|67573065|gb|BJ945889.1|BJ945889
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208382671|gb|DC923257.1|DC923257
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|162236729|gb|FC413408.1|FC413408
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|18361547|gb|BJ193613.1|BJ193613
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|162190584|gb|FC366222.1|FC366222
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|67572408|gb|BJ945232.1|BJ945232
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|67728201|gb|BJ978460.1|BJ978460
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|67719989|gb|BJ970248.1|BJ970248
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|67696449|gb|BJ956682.1|BJ956682
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208400408|gb|DC908635.1|DC908635
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208390785|gb|DC945858.1|DC945858
EST:     ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
EST: gi|208362881|gb|DC950831.1|DC950831
EST:     ACAACAAAGGTCGTTTCACCTTGCACAACATCAGCGCCGAAGAAGCCAAG                         TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA
genomic: ACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCA

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), 34 (downstream exon)
Score: 39

ATGTGATATCCATTGCCAAGACGAACGAGAACTTCCGGTTGTTGTATGACAACAAAGGTCGTTTCACCCTGCACAACATCAGCGCCGAAGAAGCCAAGgtacgtattt ... ccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactttaaagaaaaaaattcttgtactttctgaacagttttgatccttttgcagTACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG
                                      ttttgat  putative branch site (score: 39)
                                            tccttttgc  CT-rich tract
     ttaaagaaaaaaattc  TA-rich tract