Sequence
atgc intronic sequence ATGC exonic sequencegtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
Basic information
species | Physcomitrella patens |
transcript | PP1S34_404V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G41330.1 (Glycine max), 3'ss of exon 1
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
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---------------------------------------------agggacataaaatacattt-----tatctttttaaatttttactatctatg-atcctctctgat-gatatcagtatgatgagatttgattttcattctcacttgtagAGA--TTGAGATGATGAAGGAGAGGTTTGCAAAATTGTTACTTGGAGAAGATATGTCAGGTTGTGGAAATGGGGTCGCTACAGCCTTGGCTATCTCAAATGC
upper sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G16790.1 (Glycine max), 3'ss of exon 1
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgc--atcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
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--------------------------------------------------attttatctttttaatgttttaaatttttaatgt-ctatcattctctctgttgatatccgtatg---atgagttttatgatttgattttgattctcacttgta--gAGGTTGAGATGATGAAGGAGAGGTTTGCAAAATTGTTACTTGGAGAAGATATGTCAGGTTGCGGAAATGGGGTCACTACAGCCCTGGCTATTTCAAATGC
upper sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G05940.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
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--------------------------------------------------------gttagtgagaaaaaatcaaaaattgaaacttttttactcagccctaagatctcatgtgttttctttgttgttgttgtt--aatctgattgtggattagATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACTTGGTGAAGATATGTCAGGTTCTGGTAAAGGTGTGTGTACGGCTTTAGCTATCTCCAACGC
upper sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaa-cctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
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------------------------------------------------------------------gtataaaagtttccaaatttgacctcttt-tgtaaacattgatgaacactaggattcaatttcccttttgtttcctattgggttt-cagAAATTGAGATGATGAAGGAGAGATTTGCTAAGCTACTTCTCGGGGAAGACATGTCTGGTGGAGGTAAAGGGGTTTGTACGGCGCTTGCTATCTCCAACGC
upper sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctg--ttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
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------------------------------------------------------------------------------------------gtaaagtgtttaagattgtaactttcttcttt-tgtcatttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
upper sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 3'ss of exon 2
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
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--------------------------------------------------ttgggaaccacaatggaggcgtagtatggtaga---gatcttggtgggttttatttga-ggattggtacgttttcatatacatttgtgctcataatttttgtagAAGCTGAGATGATGAAGGAGAGATTTGCTAAGCTTCTACTTGGGGAAGATATGTCTGGAGGAGGGAAAGGGGTTTGTACTGCCCTTGCCATCTCAAACGCMapped 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|162256221|gb|FC432277.1|FC432277EST: AAACTTTATGTGGGAAGAAAGGAGGGAGAATAAAAAGGCTGAGCTCTCAG AAGTGGAGATGATGAAGG
genomic: AAACTTTATGTGGGAAGAAAGGAGGGAGAATAAAAAGGCTGAGCTCTCAGgtcggtaaac ... gcttctacagAAGTGGAGATGATGAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggactgatagatgcaagcgctgtgttaactgattgaacctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
ttgcttct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG