Sequence
atgc intronic sequence ATGC exonic sequenceAATCTGTCTCTTTGTATTTTTACTATGTGCGTGCATTGTGTTTGGCCACCTTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTGgtgagttttgatattcaattcaagaactcgtccttggaaagctggtgggattctaatacaggtgtgattggttaaaattctttgtgttttagtccatttc...
Basic information
species | Physcomitrella patens |
transcript | PP1S113_117V6.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S113_117V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 2
AATCTGTCTCTTTGTATTTTTACTATGTGCGTGCATTGTGTTTGGCCACCTTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTGgtgagttttgatattcaattcaagaactcgtccttggaaagctggtgggattctaatacaggtg---tgattggtta--aaattctttgtgttttagtccatttc
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CATGAACTTATTTGTGGCACTTCTTTGTGGTTGTATTGTCCTTGGCCATCTTCTTGAGGAGAATCGGTGGATGAACGAGTCTATCACTGCTCTTTTGATTgtaagtctt--cactgaccttgag--cttgtttgccataagctgttgttctaaagaatcggttaaattaaatgtttacaaaatgatctttgttgtttgccaatg-
upper sequence: PP1S113_117V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 1
AATCTGTCTCTTTGTATTTTTACTATGTGCGTGCATTGTGTTTGGCCACCTTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTGgtgagttttgatattc-----aattcaagaactcgtccttggaaagctggtg-ggattctaatacaggtgtgattggttaaaattctttgtgtt-ttagtccatttc
|| | || || | | || ||||| |||||||| ||||||| ||| | ||||| ||||||||| ||||||||||||||||||| ||| | | || ||| | || |||| | | | || |||| | ||| ||||| | || || || || |||| || ||
CATGAACATTTTCGTGGCTCTGCTTTGTGCTTGCATTGTCATTGGCCATCTTCTTGAGGAGAATCGGTGGCTGAATGAGTCTATCACTGCCCTTTTGATAgtaagtcatcatccctttataaattaatataaatactataaacaaattggtatgtatttacatacatatacattttttt----tttgttatgttattggtgtga---
upper sequence: PP1S113_117V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 1
AATCTGTCTCTTTGTATTTTTACTATGTGCGTGCATTGTGTTTGGCCACCTTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTGgtgagt--------tttgatattcaattcaagaactc-------gtccttggaaagctggtgggattctaatacaggtgtgattggt-------taaaattctttgtgttttagtccatttc---------
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CATGAACATTTTTGTGGCCCTGCTTTGTGCTTGCATTGTCATTGGCCATCTACTTGAGGAGAATCGGTGGGTGAATGAGTCTATCACTGCCCTTTTGATAgtaagtgatcatcactttataattaatataaatactataaataaattattattcatatgtatgtgtgtgcgcgcatgtgtaaattataataacataaaagactgaattaattaattaattgctatttgcag
upper sequence: PP1S113_117V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 2
AATCTGTCTCTTTGTATTTTTACTATGTGCGTGCATTGTGTTTGGCCACCTTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTGgtgagttttgatattcaattcaagaactcgtccttggaaagctggtgggattctaatacaggtgtgattggttaaaattctttgtgttttagtccatttc----------
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CATGAACTTATTTGTGGCACTTCTTTGTGGTTGTATTGTCCTTGGCCATCTTCTTGAGGAGAATCGATGGATGAACGAGTCTATCACTGCCCTTTTGATTgtaagtcttca----ctgttcttgagcttgtttgccataagctgttg---ttctaa---agaattggttaaattaaaaatttagtcctactgctaacattgtttgtcgtt
upper sequence: PP1S113_117V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT3G05030.1 (Arabidopsis thaliana), 5'ss of exon 2
AATCTGTCTCTTTGTATTTTTACTATGTGCGTGCATTGTGTTTGGCCACCTTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTGgtgagttttgata--ttcaattcaagaactcgtccttggaaagctggtgggattctaa---tacaggtgtgattggttaaaattctttgtgttttagtccatttc--------------------------
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ACTTAATCTCTTTGTTGCCCTTCTATGTGCTTGTATCGTCATTGGCCATCTTTTGGAGGAGAATCGATGGATGAACGAATCCATCACTGCTTTATTGATTgtaagtttccattattttgcgttgaatggtagctaaagaggagacggataagttttacatttttggatattatcatatcaatgtttcactttcatttttctttactgactttttaagcaattgggttgcagMapped 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|100447207|gb|CJ971506.1|CJ971506EST: TTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTG GGACTTTGCACAGGAGTTGTTGTTTTAATTTCAAGTAATGGTCAGAGTTCT
genomic: TTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTGgtgagttttg ... gatcgtgtagGGACTTTGCACAGGAGTTGTTGTTTTAATTTCAAGTAATGGTCAGAGTTCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATCTGTCTCTTTGTATTTTTACTATGTGCGTGCATTGTGTTTGGCCACCTTTTGGAGGAAAATCGGTGGATGAATGAGTCTATCACTGCTCTTCTTCTGgtgagttttgatattcaattcaagaactcgtccttggaaagctggtgggattctaatacaggtgtgattggttaaaattctttgtgttttagtccatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA