Sequence
atgc intronic sequence ATGC exonic sequence...gcaattattacgtataactggtgtcaactgggaaattgtgcgtcgaaagtggcgcgtgaaatgttctctttgtgcaacagttggcttcttttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCT
Basic information
species | Physcomitrella patens |
transcript | PP1S3_535V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S3_535V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os05g32360.1 (Oryza sativa), 3'ss of exon 4
gcaattattacgtataactggtgtcaactgggaaattgtgcgtcgaaagtggcgcgtgaaatgttctctttgtgcaacagt-tggcttcttttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCT------------------------------
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--------------------------------gtacggctttttaaaagaacgataaatattgatattcttgggttgctgcatatatttttttttatgttgaagttgtta-------tgtcgttgtat-agTCCATGGTAACAAGTACAAGGGGAGCATTTACATGGTCTTCGAGTACATGGACCATGACTTGACTGGGTTGGCAGATAGGCCTGGGATGCGTTTCACCGT
upper sequence: PP1S3_535V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 4
gcaattattacgtataactggtgtcaactgggaaattgtgcgtcgaaagtggcgcgtgaaatgttctctttgtgcaacagttggcttcttttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCT------------------------------
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-------------------------------------gtatggcacattttattcctgcaat-tccttggtttgtgggagtggttctaggttgtaat---gtctgatgcattgtcatcttgttgaaatagTCGAGGGTAACAAGTACAAGGGGAGCATCTACATGGTCTTCGAGTACATGGATCATGATCTTACTGGGCTTGCAGATAGGCCTGGGATGCGGTTCACTGT
upper sequence: PP1S3_535V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 4
gcaattattacgtataactggtgtcaactgggaaattgtgcgtcgaaagtggcgcgtgaaatgttctctttgtgcaacagttggcttcttttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCT------------------------------
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-----------gtatgtcgagcttcactcttgtgattgggctccgttactt-tgtttttagggttaagttagagcagtggt--------------gatggttcgcacgaattgttgtgtttttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGT
upper sequence: PP1S3_535V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------gcaat-tattacgta-taactggtgtcaactgggaaattgtgcgtcgaaagtggcgcg----tgaaatgttc------tctttgtgcaacagttggcttcttttgtg--aacagGACCCGAGAAAGAGGACAACATCAAGCCAGGC----GATGCGAGTAAGTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCT---------------------------------
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gcaagtactttattgtcatgtgctatgttagccaatcatgatgttagtgcattgcatgctttcctatgttggttcacttatcacgtgaggatattttcatgaacttaaaaagttacataaatattgccgcataagctggtccttactagagtaccaagaatttctgatatcaacttcattacttggggttgcagATGGTAATAAGTACAAAGGAGGCATCTACATGGTTTTTGAATACATGGACCATGATTTGACTGGTCTTGCTGATCGTCCTGGGATGAGATTTTCAGTCCCMapped 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|67704726|gb|BJ964959.1|BJ964959EST: GTTGCAACATGCGAATGTCATTAAATTGAANGAGATTGTGACCTCTAAAG GACCCGAGAAAGAGGACAACGTCAAGCCAGGCGATGCGAGTAAGTTCAANG
genomic: GTTGCAACATGCGAATGTCATTAAATTGAAGGAGATTGTGACCTCTAAAGgtagccaatg ... ttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAG
EST:
gi|67718151|gb|BJ968410.1|BJ968410EST: GTTGCAACATGCGAATGTCATTAAATTGAAGGAGATTGTGACCTCTAAAG GACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAG
genomic: GTTGCAACATGCGAATGTCATTAAATTGAAGGAGATTGTGACCTCTAAAGgtagccaatg ... ttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtggcgcgtgaaatgttctctttgtgcaacagttggcttcttttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCT
cttcttttgt CT-rich tract
aaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaattattacgtataactggtgtcaactgggaaattgtgcgtcgaaagtggcgcgtgaaatgttctctttgtgcaacagttggcttcttttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA