Sequence
atgc intronic sequence ATGC exonic sequence...tcacttgtgtgtgtatgtatcatctaattggtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
Basic information
species | Physcomitrella patens |
transcript | PP1S323_18V6.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
tcacttgtgtgtgtatg-tatcatctaattggtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgact----ggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
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-gacatgcatttatgtgatattaact--ttcgttgacccaacctattccttcccttgttttattcaa--attacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
upper sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 1
tcacttgtgtgtgtatgtatcatctaattggtttttttaaaaagtgta-ataagatga-gttgcttgagaattgcaactgactggtgggggatgtgatt-cagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
|| | || | | || | ||| | || | | ||| || |||| || ||| || || | | | | |||| ||||| || | ||||| | |||||||||||||| ||||| ||||||||||| |||||||||| || || || ||||| || || ||||| | ||
---ttttaccgaactgatactaacaccctgctctttatctcaattctgtatactatactgttggtttgcttttgtggttgttgatcatggattcttactgcagCTGGAGTTCCCTTGGAGAACATTCTATATCTTGGAGGCCCAAACATTGCTTCTGAGATTTATAACAAAGAATATGCGAATGCTCGCATATGTGGAGCTGA
upper sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 2
--tcacttgtgtgtgtatgtatcatctaattggttttt--ttaaaaagtgtaataagatgagttgcttgagaattgcaactgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
|| | | | || | || | | | || ||| | || | || || | |||| ||| | | || |||| ||||| || || |||||| | || |||||||| || || ||||||||||||||| |||| ||||| || || || |||||||| || ||||| | ||
agatacatatatatgctcaatgcttcctcctaatctccaagtatttgttgtcccctctttgattttgtatgatttattatggactattgg----tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA
upper sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
-tcacttgtgtgtgtatgtatcatctaattg-gtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgactg-gtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
||| | | | | | | |||||| ||| || || | | | || | | | ||| | | | || | | | |||| ||| |||||||| ||||| | || |||||||| |||||||||||||| || ||| | || ||||||||||| ||||||||| | |||||||| | ||
aatactcttttttatttatttcatctgattttgtattatcataggtcatagccttctta-ccatgcaataatatctattctttgcattgcaaacttgat--agCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
upper sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 1
tcacttgtgtgtgtatgtatcatctaat-tggtttttttaaaaagtg-taataagatgagttgcttgagaattgca-actgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
||| || | | | | ||||| | | | || | | | | ||||| | | ||| | |||| ||| || | ||| |||| |||||||| ||||| | || |||||||| |||||||||||||| || ||| | || ||||||||||| ||||||||| | || ||||| | ||
tcatctgattttttct-tatcagagatcatagccttctaactatgcaataatatgtttagtccttccctaattctttactctttgcgcccaaacttga--cagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
upper sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 1
-tcacttgtgtgtgtatgtatcatctaattggtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
| |||| || | | || || | | ||| | || || | | | | | | ||||| | | | |||| ||||||||| ||||| | || |||||||| |||||||||||||| || ||| | || ||||||||||| |||||||| || || || || ||
agaatttgtttgataacgaccaatggaagctggtaatttggta-gtatatctatttttatctttcctcattctcaactctttacaatgcatactttgacagCTGGAGTGCCTATGGAGAACATACTGTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCCCGAATTTGCGGAGATGA
upper sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
-tcacttgtgtgtgtatgtatcatctaattggtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
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agaatttatttg-ataccaaccaatagaagctgataatttagtagtatatctatttctatattttctcattctcaactctttacaattcatactttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGAMapped 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|18375331|gb|BJ206909.1|BJ206909EST: GGACCCTCACCCCCACATCATCACTCCTACCCAGATGATTGTGGATATGA CCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTT
genomic: GGACCCTCACCCCCACATCATCACTCCTACCCAGATGATTGTGGATATGAgtaagtcttg ... tgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaataagatgagttgcttgagaattgcaactgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
aactgac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcacttgtgtgtgtatgtatcatctaattggtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG