Sequence
atgc intronic sequence ATGC exonic sequence...aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
Basic information
species | Physcomitrella patens |
transcript | PP1S67_234V6.1 |
intron # | 39 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatg----tgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
|||| | || |||| || ||| | | | | | | || |||| | | | || || | | || ||||| || || ||||||||||| ||||| |||||||||||| | || || |||||||| ||||| || || || || | || || ||| |||||||
-------------gtaagtgcttttacataatata-tatt-ttctatttcatgagtca---tttcaa--gttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
aattatatgtgctgtaaatcgttagttctaatctagtatgactt-tgccttaggtgccaaggttt-cgatgacttcgtatggttgctacatatga--------tgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
|||| | | | | | ||||||| || || | | || | | | | | | | || | ||| ||||| | | || || ||||| ||||| ||||||||||| |||||||||||| | || || |||||||||||||| || || || || | || || ||| |||||||
-------------gtaagt-----gcttttacatagtatgttttctgtttcacatg--aggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
|||| | | || ||| | || ||| | | |||| || | || ||||| | | | |||||| | ||||| ||||| ||||| |||||||||||| | |||||||| ||||| | || ||||||||||| |||| || || | ||||||
-------------gtaagcc--cattttaaattaaataatgatttctc------gtcaagattcaaa---ctaagtatgacaatgatgctc--tattcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 35
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
|| || | | ||| || | | | ||| | | | | || || ||| ||| || || | || ||| |||||| | ||||||||||| ||||| |||||||||||| | | |||||||||||| | || ||||||||||| | || | || || | ||||||
----gtaagttcatttaatta--agcaagcaatttatttgatgtcatatca--ttttaaatttgggataactggagctgaaatcttta-ataatggccagGGTTCGTATGCATTATGGCCATCCAGATGTTTTTGATAGAGTTTTCCATATAACACGAGGTGGTATCAGCAAGGCCTCTCGAGTTATCAACATTAGTGAA
upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
| | | || | || | ||| ||| ||| | | | ||||||||| |||||||| |||||||| |||||||| ||| | || ||||||||||||||||| || || || ||| | || || || | |||||
--------------------------------------------------gtaagtctactcttggtagaacttgtagtgtta--acagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
lower sequence: EFJ05083 (Selaginella moellendorffii), 3'ss of exon 37
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
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--------------------------------------------------gtacgtctattcttggtagaacttgtagtgtta--acagtttttatgcagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAGMapped 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|162279974|gb|FC456160.1|FC456160EST: GAGCGGAGCTTTGTCACACTTGGGCAACGAGTCTTGGCAAAGCCACTGAA GGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATAT
genomic: GAGCGGAGCTTTGTCACACTTGGGCAACGAGTCTTGGCAAAGCCACTGAAgtgagtgttc ... tgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
tacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
- - - - -tgctgta
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