Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgaatctgtttacttgattgagtaatcataaagattagattttgtgaagctaagttgattggttttgttagGTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43600.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G130034_T01 (Zea mays), 3'ss of exon 2
-----------------gtaatttgaatctgtttacttgattgagtaatcataaagattagattttgtgaa--gctaagttga----ttggt-tttgttagGTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATG
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tttctattgtgatatttgtagccacaa-ctgtgcagcaactagaacacgcatccatgcccaccttcgctgattgttgacgtgtgcttctggtgttctctagGTATATAAAAGGGATAATGAATCAACTTGGCCTTGTTGTTCGAGAAGATGCTGTTGGTAACATATTTGGCCGCTG
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G34790.1 (Glycine max), 3'ss of exon 2
------------------gtaatttgaatctgtttacttgattgagtaa--tcataaagattagattttgtgaagctaag----ttgattggttttgttagGTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATG
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atataacattacttataagtaaact-attcaatatgatagatatatgagcttcaccatagtatggctttatagactttcactccttgtcttgcatctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGTCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTG
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G32850.1 (Glycine max), 3'ss of exon 2
---------------------gtaatttgaatctgtttacttgattgagtaatcataaagat---tagattttgtgaagctaagttgattggttttgttagGTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATG
|| | | || | || |||| || | |||| ||| || ||| | | | ||||||||| || | ||||| ||||||||| || |||| ||||| ||||||||||||||||||||||| ||
ctaacttttgtatgtctagcattacctatgaataaactattcaatcttgtaaagatgtcccttcatagacttt-cactccttccttgtcttgcgtctgtagGTATGTAAAAACCCAGATGGAACTTGCTGGCCTATCTGTGAGAGAGGATGCTGTTGGTAACATATTTGGTCGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgagtaatcataaagattagattttgtgaagctaagttgattggttttgttagGTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATG
agttgat putative branch site (score: 5)
ttttgtt putative PPT
taatcataaagattag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgaatctgtttacttgattgagtaatcataaagattagattttgtgaagctaagttgattggttttgttagGTATGTGAAGAATTTGATGGCACTTGCTGGTCTTACTGTTAGAGAAGATGCTGTTGGTAACATATTTGGCAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT