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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacggctctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG

Basic information

species Physcomitrella patens
transcript PP1S269_30V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S269_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os06g10280.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------------------------ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacggctctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG
| | | | | | || |||| | |||| | || | || | | || | | | ||| || |||| ||||||||||||||||| |||||||| ||||| || | || || |||||||| ||||||||||||||||| |
gtttgtgaaacatcttgagattgcaagtagtaaaagagttctgatttttttttctgtatatgtttaccgtatgcattgtgtttctaatatatccaaataaactggaaatcataatgcagttgttcatcaacttgattttatgaactatgctcctgccttgcatttgcttta-atggtattgtattgtacctt--tcctagACTTTTGATGCTGTTGATGGTAAACAAGCAAGGCGCACTAGCTCATCAAGTCCTCTAGGAGAACTTTTTGATCATG

upper sequence: PP1S269_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 4
ataactagtggcagctgcgatatttctcaat-tgacggatatggatgcagcgttaat----tatccaccctt--aagatacggctctaaacccaatcttcttca--cagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG
|| | || | || || || | | | | | ||| || | |||| | | | || | | ||| || || | ||||| ||||||||||| ||||| |||||||| ||||| || || || || |||||||| || || |||||||| ||||
---------ggggttttcggttttcctggatctaatagcttcattttttattgaaatatcacgtcaatccttccatttttttagtttacatcgaatgttgtttatgcagACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG

upper sequence: PP1S269_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 5
ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacggc--tctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG
| | | || || ||| | ||| | | | | || || ||| | || | || | ||| | | |||| |||||||||||||||||||| |||||||| || |||||||| || || || | || || || |||||||| |
-tggtttatc-catggaagacttttactacatgatgccttagtttccattctttgctataaatgattcatttattgttttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG

upper sequence: PP1S269_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 5
-ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacggctctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG
|| | | || || ||| | ||| | | | | || || ||| || | || | | | | | |||| |||||||||||||| ||||| |||||||| || |||||||| || || || | || || || |||||||| |
catggtttatt-catggaagacttttactacatgatgccttagtttccaatctttgctataattatttcatttattcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG

upper sequence: PP1S269_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacgg----ctctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG
| | || | | | ||| || || | | || || ||| ||| | | | | ||| | | | ||||| |||||||||||||||||||| ||||| |||||||||||||| || ||||| | |||||||||||||| || |
----tttgctatgattgagtagtgtttcatttattatattttggcaatgccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG

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|208353961|gb|DC914101.1|DC914101
EST:     TTCCTCGGTGGGTGCACTTTGCACATGGCATCCTTCTCTTTCTTTACCAG                         ACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGT
genomic: TTCCTCGGTGGGTGCACTTTGCACATGGCATCCTTCTCTTTCTTTACCAGgttaaacctc ... ttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGT
EST: gi|100429089|gb|BY977934.1|BY977934
EST:     TTCCTCGGTGGGTGCACTTTGCACATGGCATCCTTCTCTTTCTTTACCAG                         ACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGT
genomic: TTCCTCGGTGGGTGCACTTTGCACATGGCATCCTTCTCTTTCTTTACCAGgttaaacctc ... ttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGT
EST: gi|208363842|gb|DC943299.1|DC943299
EST:     TTCCTCGGTGGGTGCACTTTGCACATGGCATCCTTCTCTTTCTTTACCAG                         ACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGT
genomic: TTCCTCGGTGGGTGCACTTTGCACATGGCATCCTTCTCTTTCTTTACCAGgttaaacctc ... ttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagcgttaattatccacccttaagatacggctctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG
                               ctctaaa  putative branch site (score: 3)
 tcttcttcac  putative PPT
 ttaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacggctctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA