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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATATTCTGATTATCTTGTTCTCGTGGCTCGCCATCGTCTCCGCGTTCCGATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtctcctctgtttcttcgttgtgtatctttgttgcggatggggagtttgtaggtgtgatttgagggatgggagtgcttttgctaccccttcgt...

Basic information

species Physcomitrella patens
transcript PP1S123_9V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S123_9V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os07g26940.3 (Oryza sativa), 5'ss of exon 1
GTATATTCTGATTATCTTGTTCTCGTGGCTCGCCATCGTCTCCGCGTTCCGATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaa----cgcgtc-tcctctgtttcttcgttgtgtatctttgtt-gcggatggggagtttgtaggtgtgatttgagggatgggagtgcttttgctaccccttcgt
 || || ||  |  |||| ||| | |||||   | || ||||||  | |   |||    |||| | ||| ||||| ||||||||||||| |||||||||||||     ||| ||  || | | ||| |   |   |   |   ||    || || |||||||    | |  ||     |   |    | | ||| |   |      
CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccgcctcgccccccgattcattcatccatccatccattcattgacggcgagtttgctcct-tctttcattagtccgatccgttcttgattagcg-----

upper sequence: PP1S123_9V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G114911_T02 (Zea mays), 5'ss of exon 1
GTATATTCTGATTATCTTGTTCTCGTGGCTCGCCATCGTCTCCGCGTTCCGATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtctcctctgtttcttc----gttgtgtatctttgttgcggatggggagtttgtaggtgtgatttgagggatgggagtgcttttgctaccccttcgt-
 || || || ||| |||| ||||| ||||||  | || ||||||  ||| | |||    | || ||||| ||||| |||||||||||| |||||||||| ||||| || ||| || ||| ||||    ||       ||    | | |    | |   |||  ||| |   |      | |  |     |||  |||| |  || 
CTACATCCTCATTGTCTTCTTCTCCTGGCTCCTCGTCCTCTCCGTCTTCGGCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaac-cgcctcttccgttccttcccaagtcccaagcctcccctcccgcctcgta---tgtgcgtgcggggttcccatttgctgctgaattgtgaccc-tgggtg

upper sequence: PP1S123_9V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 1
GTATATTCTGATTATCTTGTTCTCGTGGCTCGCCATCGTCTCCGCGTTCCGATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtctcctctgtttcttc----gttgtgtatctttgttgcgga-tggggagtttgtaggtgtgatttgagggatgggagtgcttttgctaccccttcgt
 || ||  | ||  |||| ||||| ||||||  | || ||||||  ||  | |||    | || ||||| ||||| |||||||||||| |||||||||| |||||  | ||| |  | ||  ||    ||       ||    | |||  | |  | || ||  | | | |   |      |  |   |||||   |    |   
CTACATCATCATCGTCTTCTTCTCCTGGCTCCTCGTCCTCTCCGTCTTTGGCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaac-tgcctctttcgatttctctcaagtcccaagcctcccctccggcctcgtaaattcgtgcggg-gttcccatttgctgttgaaattttgacccggagt---

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|162251000|gb|FC426342.1|FC426342
EST:     GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|67570276|gb|BJ943100.1|BJ943100
EST:     GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|208380086|gb|DC914636.1|DC914636
EST:     GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|67570307|gb|BJ943131.1|BJ943131
EST:     GATGCNATGCCNGAACCGCATGGACTGTCGTCAACCTCNTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|208366110|gb|DC955211.1|DC955211
EST:     GATGCGATGCCGGAACCGCATGGACTGTTGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAGGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|208374713|gb|DC948671.1|DC948671
EST:     GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|208358318|gb|DC934539.1|DC934539
EST:     GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|208390884|gb|DC942216.1|DC942216
EST:     GATGCGATGCCGGAACCGCATGGACTGTTGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAGGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|67693546|gb|BJ953779.1|BJ953779
EST:     GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|208381726|gb|DC928389.1|DC928389
EST:     GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
EST: gi|162208071|gb|FC384240.1|FC384240
EST:     GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCC                         GTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC
genomic: GATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGAC

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), 35 (downstream exon)
Score: 12

GTATATTCTGATTATCTTGTTCTCGTGGCTCGCCATCGTCTCCGCGTTCCGATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtc ... ttatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGACCAAGGTGATTATGGGAAGCTTACATGGTGGGAGCAAGTGGACGATGGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATATTCTGATTATCTTGTTCTCGTGGCTCGCCATCGTCTCCGCGTTCCGATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaacgcgtctcctctgtttcttcgttgtgtatctttgttgcggatggggagtttgtaggtgtgatttgagggatgggagtgcttttgctaccccttcgt

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