Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttgaacttttcaataattttatatttttgccattacgtagtttatacgaaaactactaatcttgtagattagtcttagagtcatagctttgaatgatgttactagtgatttatgttaaatctacaatgcatcagattctaactttgtttgctttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G07230.1 (Glycine max), 3'ss of exon 2
gtgagtttgaacttttcaataattttatatttttgccattacgtagtttatacgaaaactactaatcttgtagattagtcttagagtcatagctttgaatgatgttactagtgatttatgttaaatctacaatgcatcagattctaact-ttgtttgcttt-cgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
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------------------------------------------------------------aatacctatg-agacaagccataggttt-----tgtgcataaatttgttat--attaatcttattacactaatgaat-agttattatttgttattggatttatgtgtagGTGGTCTGCGATTGCATCTCGCTTACCAGGAAGGACAGACAATGAAATAAAGAACTATTGGAACACTCACATTAGAAAAAGGCTTCTGAGAATGGGAATT
upper sequence: AT4G05100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G32090.1 (Glycine max), 3'ss of exon 2
gtgagtttgaacttttcaataattttatatttttgccattacgtagtttatacgaaaactactaatcttgtagattagtcttagagtcatagctttgaatgatgttactagtgatttatgttaaatctacaatgcatcagattctaactttgtttgctttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
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---------------------------------------------------------ttaattaatgttgttcttccattt--aaattgaagtttt-atttctgtaataaatg-tttatattaatattattatac------taatggattattggatttatgtgtagATGGTCTGCCATTGCATCTCGCTTACCAGGAAGGACTGACAATGAAATAAAGAATTATTGGAACACTCACATTAGAAAAAGGCTTCTGAGGATGGGAATT
upper sequence: AT4G05100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0203g00070.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtttgaacttttcaataattttatatttttgccattacgtagtttatacgaaaactactaatcttgtagattagtcttagagtcatagctttgaatgatgttactagtgatttatgttaaatctacaatgcatcagattctaactttg--tttgctttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
|| | | |||| | || | | || ||| | ||| | || | | | | || | | | | | | ||| | | |||| ||| |||| |||||||||||||| ||||| ||||| |||||||||| || || || || ||||| ||||| |||||||| ||||| |||||||| || || | ||||||||
---------------------------------------------------gtgagttttgttt-tcttctcttataatatataagatata---tagaacaagtggaccaaaaaataaccttgatttt-ctttac-tcactgttttgttttgattttcctttaatatagGTGGTCTGCCATTGCTGCTCGCCTGCCTGGAAGGACTGATAATGAAATCAAGAACTACTGGAACACCCACATTAGAAAAAGGCTACTGAGAATGGGAATT
upper sequence: AT4G05100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagtttgaacttttcaataattttatatttttgccattacgtagtttatacgaaaactactaatcttgtagattagtcttaga---gtcatagctttgaatgatgttactagtgatttatgttaaatctacaatgcatcagattctaactttgtttgctttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
|| | | | ||| | ||| | | ||| || | | | | || | | | | | || || || || || || |||| | | |||| ||| || || ||||| || || |||| | |||| |||||||||||||||| ||||| ||||||||||| || | | ||| | | | | | |||||||
-----------------------------------gtataaagcattttcgaagaattgagtttagcttacccatgccccgcaaatgtggcacatttctcagtacactttctttctgaaaatatttgattccgaaagcattgcacgttttttttggttggatt-----agATGGTCAGCAATCGCGGGCCACCTGCCCCAGCGAACAGACAACGAGATAAAAAATTATTGGAACACGCATTTGAAGAAACGCTTGGCACACAGGGGAATC
upper sequence: AT4G05100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S2_60V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagtttgaacttttcaataattttatatttttgccattacgtagtttatacgaaaactactaatcttgtagat-tagtcttagagtcatagc-tttgaatgatgttactagtgatttatgttaaatctacaatg-catcagattctaact--ttgtttgctttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
||| ||| | ||| || | ||| || | ||| | | | || || || | || || |||||| | || ||| | | ||| |||||||| || || || | | || | | || ||||||||||| |||||||| |||||||||||| | | || ||||| || | || |||||
------------------------------------------------------------------------gatatagaccaagacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataattcttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
upper sequence: AT4G05100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgag--tttgaacttttcaataattttatatttttg------ccattacgtagtttatacgaaaac--tactaatcttgtagattagtcttagagtcatagctttgaatgatgttactagtgatttatgttaaatctacaatgcatcagattctaactttgtttgct------ttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
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gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttatgttaaatctacaatgcatcagattctaactttgtttgctttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
ttctaac putative branch site (score: 1)
ctttgtttgctttc CT-rich tract
atgttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttgaacttttcaataattttatatttttgccattacgtagtttatacgaaaactactaatcttgtagattagtcttagagtcatagctttgaatgatgttactagtgatttatgttaaatctacaatgcatcagattctaactttgtttgctttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG