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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAATGGCCATGGCAGCGGCTCCCTCCCTCCCGCACTTCCATGGCCTTCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgcacttttccatctctcgctcctcgttgtgaattgatgctgtaactctgggttggtgataggcattgtgaagttgaatggttttggcattggt...

Basic information

species Physcomitrella patens
transcript PP1S52_45V6.1
intron # 1
splice site 5'
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|18371498|gb|BJ203100.1|BJ203100
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|100396986|gb|BY953927.1|BY953927
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|208390334|gb|DC929282.1|DC929282
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|18368808|gb|BJ200893.1|BJ200893
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|67716440|gb|BJ966700.1|BJ966700
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCNAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|208375556|gb|DC940526.1|DC940526
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|67716802|gb|BJ967061.1|BJ967061
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|18330114|gb|BJ162120.1|BJ162120
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|208372128|gb|DC940310.1|DC940310
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|67702763|gb|BJ962996.1|BJ962996
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|67718918|gb|BJ969177.1|BJ969177
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCCGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|100413633|gb|BY974914.1|BY974914
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|208371639|gb|DC932468.1|DC932468
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|100394380|gb|BY972040.1|BY972040
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
EST: gi|208376991|gb|DC911059.1|DC911059
EST:     TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTC                         CACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA
genomic: TCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCA

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: 15 (upstream exon), 21 (downstream exon)
Score: 1

GTTGCAATGGCCATGGCAGCGGCTCCCTCCCTCCCGCACTTCCATGGCCTTCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgca ... tatgaaacagCACATGGGAAAGCGGGAGCCTTCCGAGTGCGATGCGCGGCGTCAGTTTCCAGTGCCCCGAAGCGAGAAACGGATCCAAAGAAGAGGGTGGTGATTACTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAATGGCCATGGCAGCGGCTCCCTCCCTCCCGCACTTCCATGGCCTTCGCTCCACTGAGTTTCAAGCTCAGTACCCTGCACCGCCTACAGCTTCTCgtatgttgcacttttccatctctcgctcctcgttgtgaattgatgctgtaactctgggttggtgataggcattgtgaagttgaatggttttggcattggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA