Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAATACGCATTCCATTATGCTCGGCTACATGGCAGGAAGCGAGTCTCTGCCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatctcgaagttggacccgtaggttgcattgttgtccagtattggtgtataaccgaggtggtctacagaggcccttatcactgaggtgaattcgattcagctttaaaatcacttgagcagcgggtaattttaaagatgtaacagctgacatgacataaataactcgagggatgttacag

Basic information

species Physcomitrella patens
transcript PP1S199_33V6.1
intron # 3
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|67726238|gb|BJ976497.1|BJ976497
EST:     TAAAGC-AATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: TAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|162174845|gb|FC351637.1|FC351637
EST:     CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|100356789|gb|BY965281.1|BY965281
EST:     CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|67725138|gb|BJ975397.1|BJ975397
EST:     CCANTCATAAAGCAAATATCATGNAGAAGACTGATGGACTG-TTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|100394804|gb|BY989933.1|BY989933
EST:     CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|67696691|gb|BJ956924.1|BJ956924
EST:     TTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: TTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|162261041|gb|FC437435.1|FC437435
EST:     CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|208375010|gb|DC956406.1|DC956406
EST:     CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|208361101|gb|DC957552.1|DC957552
EST:     CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|162155666|gb|FC331279.1|FC331279
EST:     AAGCAAATATCATGAAGAAGACTGATGGACT-TTTTTGGAG                         TG-TGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: AAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|162261042|gb|FC437436.1|FC437436
EST:     CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
EST: gi|208367531|gb|DC954963.1|DC954963
EST:     CCATTCATAAAGCAAATNTCATGNAGAAGACTGATGGACTGTTTTTGGAG                         TGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT
genomic: CCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTT

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), 22 (downstream exon)
Score: 2

TAAATACGCATTCCATTATGCTCGGCTACATGGCAGGAAGCGAGTCTCTGCCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatct ... gatgttacagTGTTGTAGGGAAGTAGCTGCGGAGTATCCTGACATTGTGTATGAAGAAGTTATCATCGACAATTGCTGCATGATG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAATACGCATTCCATTATGCTCGGCTACATGGCAGGAAGCGAGTCTCTGCCATTCATAAAGCAAATATCATGAAGAAGACTGATGGACTGTTTTTGGAGgtatttatctcgaagttggacccgtaggttgcattgttgtccagtattggtgtataaccgaggtggtctacagaggcccttatcactgaggtgaattcgattcagctttaaaatcacttgagcagcgggtaattttaaagatgtaacagctgacatgacataaataactcgagggatgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG