Sequence
atgc intronic sequence ATGC exonic sequence...catgaagcgagtttaatatttcaaaagattaatagcttctatttcagctctgcaaccactttgcatcattccatcataacgctacgtttggcaattgcagGAGGATTTCAATTCTTGGAATTACTGGAAGATGCCACTTCCAGATATTGAAGATGAAATAAGTGTCAAGAGGTTTACAGTTCGTTTTATTTGTCTGTTAA
Basic information
species | Physcomitrella patens |
transcript | PP1S2_272V6.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_272V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os05g38710.1 (Oryza sativa), 3'ss of exon 10
catgaagcgagtttaatatttcaaaagattaatagcttctatttcagctctgcaaccactttgcatcattccatcataacgct--acgtttggcaattgcagGAGGATTTCAATTCTTGGAATTACTGGAAGATGCCACTTCCAGATATTGAAGATGAAATAAGTGTCAAGAGGTTTACAGTTCGTTTTATTTGTCTGTTAA
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--gcaagggcagctagtgtgattgtgttgtactcatgtatggtcatactccataacatgcaaattcctttttgtgctgatcatcaatgatgatgccttgcagGAAGACTACAATTCCTGGAATTACTGGAAGATGCCATTGCCAGATGTTGATCTGTAGTGTAGTTCTAACAAACACAGAAGTAGATAACACTAGATTCTGC
upper sequence: PP1S2_272V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G154366_T01 (Zea mays), 3'ss of exon 9
catgaagcgagtttaatattt--caaaagattaatagcttctatttcagctc--tgcaaccactttgcatcattccatcataacgctacgttt---ggcaattgcagGAGGATTTCAATTCTTGGAATTACTGGAAGATGCCACTTCCAGATATTGAAG-ATGAAATAAGTGTCAAGAGGTTTACAGTT-CGTTTTATTTGTCTGTTAA
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------tcccgtatagtatttgtcagcagttcaagtgtgctttacacgttttattgcaattgcctt-tattttttggtcctgatggcaagttcttggtcgaattcagGAGGACTACAATGCTTGGAATTACTGGAAGATGCCATTGCCTGATGTTGATTTGTGAGGTACAAGTCGAGTC-TGCACAACAGCACTGCACTAATTTTATG-
upper sequence: PP1S2_272V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA17G36130.1 (Glycine max), 3'ss of exon 11
-------catgaagcgagtttaatatttcaaaagattaatagcttctatttcagctctgcaaccactttgcatcattccatcataacgct-acgtttggcaat--tgcagGAGGATTTCAATTCTTGGAATTACTGGAAGATGCCACTTCCAGATATTGAAGATGAAATAAGTGTCAAGAGGTTTACAGTTCGTTTTATTTGTCTGTTAA
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gtttaattctgaaggaacttt--ctctaaaaaaattccctacaaactcctaaggatttgtctgtgatgtaccttattttttggccttgttcatgctgaatattggtgcagGAGGATTTTAATTCATGGAATTACTGGAAGTTACCT------GAGACCTCTTCTGCTACAAATATTTGA-------------------------------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|162273449|gb|FC449898.1|FC449898EST: TGCACAAACTTGTTGATGATATGTTTCCTCCTCAGAGTTGCACAGAACAG GAGGATTTCAATTCTTGGAATTACTGGAAGATGCCACTTCCAGATATTGAA
genomic: TGCACAAACTTGTTGATGATATGTTTCCTCCTCAGAGTTGCACAGAACAGgtatatgctc ... gcaattgcagGAGGATTTCAATTCTTGGAATTACTGGAAGATGCCACTTCCAGATATTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctctgcaaccactttgcatcattccatcataacgctacgtttggcaattgcagGAGGATTTCAATTCTTGGAATTACTGGAAGATGCCACTTCCAGATATTGAAGATGAAATAAGTGTCAAGAGGTTTACAGTTCGTTTTATTTGTCTGTTAA
tcataac putative branch site (score: 2)
atcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgaagcgagtttaatatttcaaaagattaatagcttctatttcagctctgcaaccactttgcatcattccatcataacgctacgtttggcaattgcagGAGGATTTCAATTCTTGGAATTACTGGAAGATGCCACTTCCAGATATTGAAGATGAAATAAGTGTCAAGAGGTTTACAGTTCGTTTTATTTGTCTGTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG