Sequence
atgc intronic sequence ATGC exonic sequencegtacgttgtgtaggtgtccagcattgtgagattgtggtgcgaattacgtcttggtagtgggaattactcaaatttttagctttttctgaacagGAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCATTCAGCAGCTTCATGATCATCGTGTTGTCCTCGTCAACCAAGACTCGTT
Basic information
species | Physcomitrella patens |
transcript | PP1S83_234V6.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S83_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
gtacgttgtgtaggtgtccagcattgtgagattgt----ggtgcgaattacgtcttggtagtgggaattactcaaatttttagctttt----tctga-acagGAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCATTCAGCAGCTTCATGATCATCGTGTTGTCCTCGTCAACCAAGACTCGTT
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-tacttgatg-aggtcctaaatttggataccttgttttcaattcttacaacttttcttttatcttaatgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG--------
upper sequence: PP1S83_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 2
--------gtacgttgtgtaggtgtccagcattgtgagattgtggtgcgaattacgtcttggtagtgggaattactcaaatttttagctttttctgaacagGAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCATTCAGCAGCTTCATGATCATCGTGTTGTCCTCGTCAACCAAGACTCGTT
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ttcatgaggtcctaagtttggttaccttgttttcaattcttacaacttttcttttatcttaatgattcttactcactcattttttgtcatatgatg--caggTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAGG-------
upper sequence: PP1S83_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ31180 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------------------------------------------------------------gtac-gttgtgtaggtgtccagcattgtgagattgtggtgc--gaattac-----gtcttggtagtgggaattactcaaatttttagctttttctgaacagGAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCATTCAGCAGCTTCATGATCATCGTGTTGTCCTCGTCAACCAAGACTCGTT
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gtaaatctcgcttcgatcgattcttcatgcatcgccgcagctcggggcgttctcgagctcagattcctgtcggattccgagctttgaagcactgaagttcccgcattgtttgttgtgcgatcgtttctttggaattcctcggagccttgattcttttcttttgttgatttccttgtttcttcttggcagGTGTTGCTGGCGGTACTGCCTCCGGAAAGACCACGGTGTGTAACATGATCATACAGCAGCTACACGATCATAGGGTGGTGCTCGTGAATCAG--------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|100353505|gb|BY964840.1|BY964840EST: ATACCCGGCTACAAAACATAAAGGAGCTAACAAAGTTCCATTTATAATTG GAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCA
genomic: ATACCCGGCTACAAAACATAAAGGAGCTAACAAAGTTCCATTTATAATTGgtacgttgtg ... ttctgaacagGAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgaattacgtcttggtagtgggaattactcaaatttttagctttttctgaacagGAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCATTCAGCAGCTTCATGATCATCGTGTTGTCCTCGTCAACCAAGACTCGTT
tttttagctttttct CT-rich tract
aattactcaaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgttgtgtaggtgtccagcattgtgagattgtggtgcgaattacgtcttggtagtgggaattactcaaatttttagctttttctgaacagGAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCATTCAGCAGCTTCATGATCATCGTGTTGTCCTCGTCAACCAAGACTCGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT