Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgttgaatgatttcttgaagattctttgctatggttattgcttatattaagtcttatctggatgacgcacatttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
Basic information
species | Physcomitrella patens |
transcript | PP1S31_77V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S31_77V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
gtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgtt-gaatgatttcttgaagattctttgctatggttattgcttatattaagtcttatctggatgacgcacatttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
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------------------------------------------------gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaacc--atggcacactt-------agGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
upper sequence: PP1S31_77V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G008556_T01 (Zea mays), 3'ss of exon 6
gtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgttgaatgatttcttgaagattctttgctatggttattgcttatattaagtctta--tctggatgacgcacat--ttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
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---------------------------------------------gtaacaaactatcatttgattacttcatttgccttc--aaattcgtgtcattttttacacttttcacatgaacacttgattcatgcttatgcttatgattttattagGAAGAAAAGAGAACACTTGACCGTGAACTTGCACGTGCAAAAGTTACAGCAAACAGAGTTGCTTCTGTTGTTGCTAATGAGTGGAAAGATTCTAATGACA
upper sequence: PP1S31_77V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA15G12490.1 (Glycine max), 3'ss of exon 6
gtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgttgaatgatttcttgaagattctttgctatggttattgcttatattaagtcttatctggatgacgcacatttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
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------------------------gtaggcata-tcttattggatactg----acattttgagcttaatttc--tgatatattgatt-ttctgcattctggtcgatcaatgtagtga--cataatt---taacccaaatttt---cagGAGGAGAAAAGGACACTGGAGAGGGAGCTAGCAAGGGTAAAAGTTTCAGCCAACAGAGTTGCAACTGTTGTGGCGAATGAGTGGAAGGATGAGAATGACA
upper sequence: PP1S31_77V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G01560.1 (Glycine max), 3'ss of exon 8
gtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgttgaatgatttcttgaagattctttgctatggttattgcttatattaagtcttatctggatgacgcacatttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
| |||| || | | | |||| | | | | | ||| | | || || || | | ||| | | | || ||| | || || |||| ||||| | ||| | |||| |||||||||| | || ||| ||| || |||| |||||||||||| |||||| || |||||||||||||||| |||||||
----------------------gtaggcatat-cttatggccactgccattatgaact-taattttggatatattggctttctgcatttcggttggtctaagcagtgacatgatt--------------taacacaaatttt---cagGAGGAGAAAAGGACACTGGAGAGGGAGCTAGCAAGGGTAAAAGTTTCAGCCAACAGAGTTGCAACTGTTGTGGCTAATGAGTGGAAGGATGAGAATGACA
upper sequence: PP1S31_77V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv08s0007g05140.t01 (Vitis vinifera), 3'ss of exon 6
gtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgttga-atgatttcttgaagattctttgctatggttatt-gcttatattaagtcttatctggatgacgcacatttgaaac------agGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
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------------------------------------------------gtaagtactattattcttgcactcctatagttatttcaaaatacctggtgaccatcctgaggatataacaagtctg--caagctgcttctaacttcaagctcctgtagGATGAGAGAAAAATTTTGGACCGGGAACTATCTCGTGCAAAGGTTACTGCAAATCGAGTTGCTGTTGTTGTTGCAAATGAATGGAAAGATGCCAATGACA
upper sequence: PP1S31_77V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 6
gtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgttgaatgatttcttgaagattctttgctatggttattgcttatattaagtcttatctggatgacgca--catttga--aacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
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----------------------------------------------------------------------------------------------gtagtgccgccagccacctttgggtcgcactcaccccacattgtctttttaccattagGAAGAGAAACGGACGCTTGAGCGGGAACTGGCGCGTGCCAAGGTAACAGCAAACAGAGTGGCAGTCGTCGTTGCAAACGAATGGAAGGATGCAAACGACAMapped 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|100441798|gb|BY962889.1|BY962889EST: CTGCTGTAAATGCAGCCCGAGACTACCAACGACAGGCACAAGAGTTATTG GAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCT
genomic: CTGCTGTAAATGCAGCCCGAGACTACCAACGACAGGCACAAGAGTTATTGgtaaaattta ... tttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctatggttattgcttatattaagtcttatctggatgacgcacatttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
ttattgcttatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatttatggttttcggggttgaaaatattctccttgtgaatgccgcgagaagttattacgttgcgttgaatgatttcttgaagattctttgctatggttattgcttatattaagtcttatctggatgacgcacatttgaaacagGAAGGGAAGAAGACATTGGAGAGGGAATTGGCGCGGGCGAAAATTACAGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG