Sequence
atgc intronic sequence ATGC exonic sequenceCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtag
Basic information
species | Physcomitrella patens |
transcript | PP1S168_104V6.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv18s0089g01080.t01 (Vitis vinifera), 5'ss of exon 3
----CAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtag
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GCCATGAGCTTTGGGGGCTCAAATATAGACCCAACAGCATGGGAAGACAAGAAGTGCAGAGGAGAATCCAGATTTCCAGCCCAGgtagga----aaatttatccatt------cacccatccaaatattttcac---caattttcaattttttgaaagacttacagtgaatgaagggtgat------aataatggaatgatttcag
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 4
----CAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctcaaagcattgcgatgttaaatagt-gattcacggtttgccagatacaaat-ttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtag
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GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAGgtaaaatatcattg----atgaactgaaacacttaaattatcattctcaagactcccttactgagtcatag-tatttcatttctc---ccaataaatag-------------------------
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 3
----CAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccag-atacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtag
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GCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAGgtttgtctt-----cacttctttctcatttgcttctcgagcgtgtgtgaggatccgggcttaacttt---------ctctcgctttgtcctctccag--------------------------
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ24245 (Selaginella moellendorffii), 5'ss of exon 3
----CAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtag
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GCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAGgtttgtctctcgttttctaggagaatagaaagctttttcttgttcttgagctgcaag---agctacaaaggaaaacccatcgtgatcccatacag---------------------------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|22132955|gb|BQ827456.1|BQ827456EST: CCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG GTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTT
genomic: CCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctc ... ttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtag
- - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA