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

gtttgctttacattcccgtttgagatcctctcccggttagccgaggttttgttttgtgagggtaagcttttatcctgatgagttgatgttgaacgctggtggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGACAATTCATACCAG

Basic information

species Physcomitrella patens
transcript PP1S12_267V6.1
intron # 1
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|162197427|gb|FC372805.1|FC372805
EST:     CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAG                         TCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
genomic: CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAGgtttgcttta ... tggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
EST: gi|100364148|gb|BY966739.1|BY966739
EST:     CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAG                         TCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
genomic: CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAGgtttgcttta ... tggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
EST: gi|162171600|gb|FC347541.1|FC347541
EST:     CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAG                         TCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
genomic: CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAGgtttgcttta ... tggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
EST: gi|18363255|gb|BJ195327.1|BJ195327
EST:     CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAG                         TCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
genomic: CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAGgtttgcttta ... tggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
EST: gi|100445813|gb|CJ970112.1|CJ970112
EST:     CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAG                         TCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
genomic: CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAGgtttgcttta ... tggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
EST: gi|208387491|gb|DC933354.1|DC933354
EST:     CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAG                         TCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
genomic: CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAGgtttgcttta ... tggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGAC
EST: gi|18363594|gb|BJ195666.1|BJ195666
EST:     CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAG                         TCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAG
genomic: CAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAGgtttgcttta ... tggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAG

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: 19 (upstream exon), 26 (downstream exon)
Score: 5

CGTCAGGAGCCAGGCACAGGTGGGGTCTATGGGGAGGGATGATCAATCCACAACAGTATCGCCATTGGCCAAGTACAAATTGGTGTTTCTCGGGGATCAGgtttgcttta ... tggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGACAATTCATACCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgagggtaagcttttatcctgatgagttgatgttgaacgctggtggttggcagTCTGTGGGCAAGACGAGTATCATCACACGCTTTATGTATGACAAGTTTGACAATTCATACCAG
             ttttat  TA-rich tract