Sequence
atgc intronic sequence ATGC exonic sequence...gttcatttatatccacgtgtgcgattagtttaccttctgatttgtaacttgttgaaaattcctcatctgtaaactgacagtggcagtactgcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA
Basic information
species | Physcomitrella patens |
transcript | PP1S135_17V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 6
gttcatttatatccacgtgtgcgattagtttaccttctgatttgtaacttg----ttgaaaattcctcatctgtaaactgacagtggcagtactgc-ttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA
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--taagctgtatcattgaattaaagtggtca--tgtcaaatttatattttagtacttaaattttctgaattcgtggatttaaccatgta-tactgcactttgcagCATAGAGTTTGACTGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCCCGGCGCATCAAAGTTTTTGACTTTTCTGCT
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 6
-gttcatttatatccacgtgtgcgattagtttaccttct-gatttgtaacttgttgaaaattcctcatctgtaaactgacagtggcagtactgcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA
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ctatcctttttcttgatat-tattgttgttttaatatgtagaagttagacagaataaattttctgaattcatggatttaacatgtatattgcactt-tgcagCATAGAGTTTGACCGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCGCGGCGCATCAAAGTTTTTGACTTTTCTGCT
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------------------------gttcatttatatccacgtgtgcgatta-gtttaccttctgatttgtaacttgttgaa-aattcctcatctgt-aaactga-cagtggcagtactgcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA
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gtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccctttttgctgttgttgaattgttaatttgcattcatcatattaattgtacttcagtaaataatgaacaaactgttgagttgagtatttcccatattttct-tgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 6
----------gttcatttatatccacgtgtgcgattagtttaccttctgatttgtaacttgttgaaaattcctcatctgtaaactgacagtggcagtactgcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA
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acaccatctaagttgtttgtatgtgtgtgtgtgtgtttgttatctggtattgtgtga-ttatt--aaattactgaact------tgtcattgctcatgccttattt-cagCATAGAATTTGACTGTGATGATGAGTTGTTTGCTACTGCTGGAGTTTCAAGGCGCATAAAGGTTTTCGACTTCTCTTCGMapped 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|100393347|gb|BY989832.1|BY989832EST: CATTCTTC-AATATTGTTTCAAG CATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAG
genomic: CATTCTTCAAATATTGTTTCAAGgtaggactgt ... gcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAG
EST:
gi|100353725|gb|BY983279.1|BY983279EST: CTTCAAATATTGTTTCAAG CATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAG
genomic: CTTCAAATATTGTTTCAAGgtaggactgt ... gcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttgttgaaaattcctcatctgtaaactgacagtggcagtactgcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA
aactgac putative branch site (score: 2)
ttgaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcatttatatccacgtgtgcgattagtttaccttctgatttgtaacttgttgaaaattcctcatctgtaaactgacagtggcagtactgcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa