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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcttatcttcgcctgacgttattccacttaagtgcatttgttttgttcttagattctcttggagggatacccttacttgagcgtcctcaggatgccttctattgtttcagtgctgtccgtgaatctctctctctgctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCTGCCTGCGTTTCCCCGGACAGCTCAACTCTGACCTGAGAAAGTTGGCGGT

Basic information

species Physcomitrella patens
transcript PP1S252_90V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S252_90V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ35740 (Selaginella moellendorffii), 3'ss of exon 2
gtaagctcttatcttcgcctgacgttattccacttaagtgcatttgttttgttcttagattctcttggagggatacccttacttgagcgtcctcaggatgccttctattgtttcagtgctgtccgtgaatctctc-tctctgctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCTGCCTGCGTTTCCCCGGACAGCTCAACTCTGACCTGAGAAAGTTGGCGGT
| | |||| ||||| || || | | | | | || || | ||||||||||| | ||||| | ||||| || || |||||||| || || |||||||| ||||||||||| || |||||||| ||||| | ||| |||| ||
-------------------------------------------------------------------------------------------------gtacgttctcctgtttt-gtttggtatataagttaagagtgtttgtttcatccagTTGGAGATCTAAACCATCTCATCTCCGCAACCATGAGCGGGATCACTTGCTGCCTTCGTTTCCCCGGGCAACTCAACTCGGACCTCCGGAAGCTGGCCGT
















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|162181753|gb|FC357352.1|FC357352
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|208355066|gb|DC926717.1|DC926717
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGNGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|208364162|gb|DC943418.1|DC943418
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGANCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|162181763|gb|FC357362.1|FC357362
EST:     GCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|162181456|gb|FC358070.1|FC358070
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|208382468|gb|DC928002.1|DC928002
EST:     TGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCNTCCNT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCANTACGTGC
genomic: TGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCC-Tgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGC
EST: gi|100390406|gb|BY952814.1|BY952814
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|100413051|gb|BY992564.1|BY992564
EST:     GGCTCTGTACGACATTTGCTTTANGACACTGAAGCTCATTACTCCCTCTT                         TTGGAGATTTGAAC-ACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|162228569|gb|FC404466.1|FC404466
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|162250828|gb|FC426872.1|FC426872
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|162176333|gb|FC353518.1|FC353518
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|208386892|gb|DC956903.1|DC956903
EST:     GACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCCT                         TNGGAGA-TTGNANCCACTTGATCTTTGCGACGATGAGCGGCATTACGTG
genomic: GACATTTGCTTTAGGACACTGAAGCTCATTACTCCCT-CCTgtaagctctt ... ctttgtgcagTTGGAGATTTG-AACCACTTGATCTCTGCGACGATGAGCGGCATTACGTG
EST: gi|162190322|gb|FC365336.1|FC365336
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|162163453|gb|FC339987.1|FC339987
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCG
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCG
EST: gi|162156448|gb|FC332680.1|FC332680
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTG
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTG
EST: gi|162165264|gb|FC340791.1|FC340791
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
EST: gi|100446052|gb|CJ970351.1|CJ970351
EST:     GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCT                         TTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT
genomic: GGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCT

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), 25 (downstream exon)
Score: 13

GTACATCAGTTAGTAGAAAATGCTGATGAGTGCATGGTGCTGGACAACGAGGCTCTGTACGACATTTGCTTTAGGACACTGAAGCTCATTACTCCCTCCTgtaagctctt ... ctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCTGCCTGCGTTTCCCCGGACAGCTCAACTCTGACCTGAGAAAGTTGGCGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgccttctattgtttcagtgctgtccgtgaatctctctctctgctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCTGCCTGCGTTTCCCCGGACAGCTCAACTCTGACCTGAGAAAGTTGGCGGT
                                 tctctctctctgcttt  CT-rich tract
 tattgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcttatcttcgcctgacgttattccacttaagtgcatttgttttgttcttagattctcttggagggatacccttacttgagcgtcctcaggatgccttctattgtttcagtgctgtccgtgaatctctctctctgctttgtgcagTTGGAGATTTGAACCACTTGATCTCTGCGACGATGAGCGGCATTACGTGCTGCCTGCGTTTCCCCGGACAGCTCAACTCTGACCTGAGAAAGTTGGCGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA