Sequence
atgc intronic sequence ATGC exonic sequencegttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
Basic information
species | Physcomitrella patens |
transcript | PP1S4_73V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 5
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatat-tttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
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-----------------tacag-cattagtgtgttatataca-ggctctctgtttatgattctcaagttatatggatgttagttaaagagctgaaacttcagttatcaattttgtacagGATGTTACGCTTCATGACCTTGATGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGACAGATGATGAAGCCACGGAAAACTG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
gttagtgctatgattattatgctcgt-tgcagtgtagccctcttgattctttatacagtatcctttgtatattttatg----cttgtaatcttatgcccatttctatgtgttatg-gtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
|| | |||||||| || | ||||| | | ||| | || || |||| | | | || | | |||| ||| || | | ||||||| || || ||||| || || ||||||||||||| || ||||||||||||||||| |||||| | ||||| || |||||||| || || |||||||
----------------------tcatatgcagtgttagtgcattcaatctttctgct-tatggctcttaagttatatggaagttaatgaatataggaaaacttctcc-tgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
|||| ||| | | || | ||| ||| | | | | ||| | | | | || | | | | ||| ||| |||||||||| || ||||| || ||||| |||||||||| || ||||| ||||||||||| |||||| | |||||||||||||||||||| || |||||||
-----------gattttta-ataagaattaatgcttgtat-ttgcgtctcaacatgg-aggcttcatgtgctcttgttctgaag----aggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 5
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
|| || | | || || || | | | | || | | | |||| || || | || | || | || || || | || | |||||||||| |||||||| || ||||| |||||||| | || ||||| ||||||||||| |||||| | ||||||||||||||||| || || |||||||
--------taagaat-taattcttgtatttgcatctcaacatggaggcctcct---gtattctatgc---tcttgttctgaagaggaaataacctcctcatcattttttt---tgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
| ||| || ||||| | |||| | | | || | ||| | ||| | |||||| |||| ||| |||| | | | ||||||| || || |||||||| |||||||| ||||| || |||||||| || |||||||| |||| ||||||| ||||||||||| || | || || |
----------------agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtat-tgttgttct-taaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaa--tcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
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-------------tgagtg-gcttgtactagtgtactctgtaagaatgtgttc----tagacattgaatattgtatatttctgatttcttattgtgatttggat-tgttgttct-taaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------gttagtgctatgattattatgctcgttgcagtgtagccc------tcttgattc-tttatacagtatcctttgtat---attttatgcttgtaatcttatgcccattt---ctatgtg-ttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
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gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttat-gcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
||| ||| || || | || | || | ||||| | || || | | | ||| || || ||||| | | | | ||||||| || || ||||| || |||||||||||||| || |||||||| || ||||||||||||||| | ||||| ||||||||||| || | || || |
-------ctaaagttaca----tctttataaggtgtggtttcagag-----acacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaat---cagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 5
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
||| ||| | | | | | | | | | |||| ||| ||||| ||||| || ||||||||||||||||||||||| || |||||||| || |||||||| | ||||||||||| ||||||||||| || |||||||
--------------------------------------------------------gtactaactgtgaaga--aagggtccagtttctcttcacacagcaagtgtgggtgtatgtagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTG
upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 5
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
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--------------------------------------------------------gtactaactgtg-atgaaagggtccagtttctcttcaca---cagcaagtgggtgtattcagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGMapped 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|162237933|gb|FC412534.1|FC412534EST: ATGTGCCTTTACCAAAAGGAGAAGTTCACAAAAAGAAAGAGATTGTTCAG CATGTCACGCTCCATGATCTAGATGCTGNCAA-TGCTCGCCCTCAA
genomic: ATGTGCCTTTACCAAAAGGAGAAGTTCACAAAAAGAAAGAGATTGTTCAGgttagtgcta ... tggtacatagGATGTCACGCTCCATGATCTAGATGCTG-CAAATGCTCGCCCTCAA
EST:
gi|162252178|gb|FC425856.1|FC425856EST: ATGTGCCTTTACCAAAAGGAGAAGTTCACAAAAAGAAAGAGATTGTTCAG GATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGC
genomic: ATGTGCCTTTACCAAAAGGAGAAGTTCACAAAAAGAAAGAGATTGTTCAGgttagtgcta ... tggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
tattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG