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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgggttacgttaatagttctcgttcttttgggtgcgaattgctgcttcagtgcggttaaattttagggttttaatgtgaattgctgaacgttgcagtgtccctgatgctgaatttagccctctgcgtgtggctctggttgtgttttttcattctcattttgttttattttttccttttctgttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTCTACGATTTGCTTCGGCTTTGCGGCTTCAACAGCCGCGTTACTACTCGCA

Basic information

species Physcomitrella patens
transcript PP1S4_13V6.2
intron # 2
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|162242113|gb|FC415807.1|FC415807
EST:     CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAG                         TGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
genomic: CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
EST: gi|37821216|gb|BJ579282.1|BJ579282
EST:     CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAG                         TGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
genomic: CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
EST: gi|67692351|gb|BJ952584.1|BJ952584
EST:     CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAG                         TGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
genomic: CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
EST: gi|162190053|gb|FC366627.1|FC366627
EST:     CCTAAGCAGGACATTCGTCTTTTTATCAATTGTNCGGGGGGTTCTATCAG                         TGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
genomic: CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
EST: gi|18339814|gb|BJ171841.1|BJ171841
EST:     CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAG                         TGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
genomic: CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
EST: gi|37827419|gb|BJ585431.1|BJ585431
EST:     CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAG                         TGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
genomic: CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
EST: gi|162206018|gb|FC382803.1|FC382803
EST:     CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAG                         TGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
genomic: CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
EST: gi|162224723|gb|FC401971.1|FC401971
EST:     CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAG                         TGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
genomic: CCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC
EST: gi|208379329|gb|DC918987.1|DC918987
EST:     AGCANGACATTCGTC-TTTTATCAATTGTCC-GGGGGCTCTATCAG                         TGCTGCCATNGGTATCTTTGATGCCANGCAGCTGTGTAAGTGTGATATTTC
genomic: AGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTC

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: 10

TTGTGGCTGACTCCATTATCAGCCAGTTGCTGCTCCTGGACGCCATCGACCCTAAGCAGGACATTCGTCTTTTTATCAATTGTCCGGGGGGTTCTATCAGgtatttgggt ... ttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTCTACGATTTGCTTCGGCTTTGCGGCTTCAACAGCCGCGTTACTACTCGCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtgttttttcattctcattttgttttattttttccttttctgttttttgcagTGCTGCCATGGGTATCTTTGATGCCATGCAGCTGTGTAAGTGTGATATTTCTACGATTTGCTTCGGCTTTGCGGCTTCAACAGCCGCGTTACTACTCGCA
       tttttcattctcattt  CT-rich tract
      ttttttcattctcatt  TA-rich tract