Sequence
atgc intronic sequence ATGC exonic sequence...tgaaacctactgcatttctgttgtaacatgcgaggtgtcatggattcaggggcaatgtcggtgctaggtaagataacttgtgtctattatgcacgctcagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S22_429V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 2
----tgaaacctactgcatttctgttgtaacatgcgaggtgtcatggattcaggggcaatgtcggtgctaggtaagataacttgtgtctattatgcacgctcagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
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gtgctgaaac--actggctctttcatgaactaca-aaagcgtggcagaattatccaactgatctcctcctcacattttcccctgaaatttgaatttgttc-cagGTCAGAGTCTGTAGGGAGAAAACTAGTGATCATGTATATGCAATGAAGAAGCTGAAAAAATCAGAGATGCTTCGTAGAGGCCAG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------------tgaaacctact-------gcatttctgttgtaa---catgcgaggtgtcatggatt--caggggcaatgtcggtgctaggtaagata-acttgtgtctattatgcacgct-cagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
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gtaacatctcttttatagatcatagtctgttactctgttttctcagcctctcattggcatgcatcatcttgaaatgttctctgtgatgcatccttcttgaaaggtcttcttaggccattttttttaccacagctaatttttcaaaaaagtatggcatgctaatttttctctttctctttgcagGTTAGGATCTGTAGGGAGAAGGGAACAGGCAATGTCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 3
tgaaacctactgcatttctgttgtaacatgcgaggtgtcatggatt-caggggcaatgtcggtgctaggtaagataacttg----tgtctattatgcacgctcagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
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----atttgtagt-tattagtagaaatacaaatggcgtattcaatagctgttaaactcttagttatagggactttaatgtgaatgtatttgctgtaaccatgcagGTGAGACTTTGCAGAGAAAAAACTACTGGCCATGTGTATGCCATGAAAAAGCTCAAGAAATCAGAGATGCTTCGGAGGGGCCAG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 2
----tgaaacctactgcatttctgttgtaacatgcgaggtgtcatggattcaggggcaatgtcggtgctaggtaagataacttgtgtctattatgcacgctcagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
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atctttttctttcattcagctctatcttgaatttgatcctgtgctgtatccttgcctatcatttgctcattattag-tacattgttttatttgtg---gtgcagGTAAGAGTCTGTAGAGAGAAGACAACGGGTAATGTGTATGCAATGAAAAAGCTTAAGAAGTCAGAGATGCTTCGACGAGGCCAG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 2
tgaaacctactgcatttctgttgtaacatgcgaggtgtcatggattcaggggcaatgt--cggt--gctaggtaagataacttgtgtcta-ttatgcacgct-cagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
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----gtttgtggaaaattttctgcactgtctgt--tttctttgatgctgttataacatttcatttaacttgattgcaccccttgttcttacttttctgttctgtagGTTAGAGTCTGCAGGGAGAAGAAAACCGGCCATGTATATGCCATGAAGAAGCTTAAGAAATCAGAGATGCTTCGAAGGGGCCAGMapped 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|162170612|gb|FC347108.1|FC347108EST: TGGAAGATTTTGAATTGCTAACCATCATCGGGCGTGGCGCATTTGGGGAG GTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAG
genomic: TGGAAGATTTTGAATTGCTAACCATCATCGGGCGTGGCGCATTTGGGGAGgtatgtgtcc ... gcacgctcagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaggggcaatgtcggtgctaggtaagataacttgtgtctattatgcacgctcagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
agataac putative branch site (score: 3)
taagataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaaacctactgcatttctgttgtaacatgcgaggtgtcatggattcaggggcaatgtcggtgctaggtaagataacttgtgtctattatgcacgctcagGTGAGGTTATGCCGAGAGAAATCAAGTACAACTGTGTATGCCATGAAGAAGCTGAAGAAGTCCGAGATGCTTCGGAGAGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - -tactgca
- - - - - - - - - - - - aacatgc