Sequence
atgc intronic sequence ATGC exonic sequencegtatctaattacagtctttcacttggatcgtgcacatgtagcttaggaatcaccgtatgatgtttggttctcattcggtgaattttcatgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCTAAGGCAGTTGGATGGGGTGTTATGGTCAGTCACCGAAGTGGAGAAACGG
Basic information
species | Physcomitrella patens |
transcript | PP1S83_55V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S83_55V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 4
gtatctaattacagtctttcacttggatcgtgcacatgtagcttag-gaatcaccgtatgatg-tttggttctcattcggtgaattttc---atgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCTAAGGCAGTTGGATGGGGTGTTATGGTCAGTCACCGAAGTGGAGAAACGG
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-tagttactggtaattgttc-tatggttgatcatcatatctcctaatgaaatatttcatgttgatcctgatcttatcttaatatttacccaaatgattgcagGTTAACCAGATAGGCACCGTGACTGAATCCATTCAAGCTGCACTAGACTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAG
upper sequence: PP1S83_55V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26490 (Selaginella moellendorffii), 3'ss of exon 5
gtatctaattacagtctttcacttggatcgtgcacatgtagcttaggaatcaccgtatgatgtttggttctcattcggtgaattttcatgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCTAAGGCAGTTGGATGGGGTGTTATGGTCAGTCACCGAAGTGGAGAAACGG
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----gtaagcacggtgtcgc-cttccatcattt--------ctcatgga--atcgaatccttttttttttcttttctttcgctttttg------cagGTGAATCAGGTCGGCTCCGTGACTGAATCCATCCAAGCAGCTTTGGATTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCG
upper sequence: PP1S83_55V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26799 (Selaginella moellendorffii), 3'ss of exon 4
gtatctaattacagtctttcacttggatcgtgcacatgtagcttaggaatcaccgtatgatgtttggttctcattcggtgaattttcatgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCTAAGGCAGTTGGATGGGGTGTTATGGTCAGTCACCGAAGTGGAGAAACGG
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----gtaagcacggtgtcgccttccatcatttctcatggaat---agaatcctttt----ttttttcttttctttcgct---ttttg-------cagGTGAATCAGGTCGGCTCCGTGACTGAATCCATCCAAGCAGCTTTGGATTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCGMapped 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|67698782|gb|BJ959015.1|BJ959015EST: AAATTGCTGAAGCTATTTCGAAGAAGGCTTGTAATGCCCTCTTATTGAAG GTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCT
genomic: AAATTGCTGAAGCTATTTCGAAGAAGGCTTGTAATGCCCTCTTATTGAAGgtatctaatt ... atgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCT
EST:
gi|67723958|gb|BJ974217.1|BJ974217EST: AAATTGCTGAAGCTATTTCGAAGAAGGCTTGTAATGCCCTCTTATTGAAG GTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCT
genomic: AAATTGCTGAAGCTATTTCGAAGAAGGCTTGTAATGCCCTCTTATTGAAGgtatctaatt ... atgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaggaatcaccgtatgatgtttggttctcattcggtgaattttcatgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCTAAGGCAGTTGGATGGGGTGTTATGGTCAGTCACCGAAGTGGAGAAACGG
ttttcat CT-rich tract
aattttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctaattacagtctttcacttggatcgtgcacatgtagcttaggaatcaccgtatgatgtttggttctcattcggtgaattttcatgcattcagGTGAACCAAATTGGGTCTGTGACGGAGTCGATTCAAGCTGCTTTGGACTCTAAGGCAGTTGGATGGGGTGTTATGGTCAGTCACCGAAGTGGAGAAACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA