Sequence
atgc intronic sequence ATGC exonic sequence...ctcttagtaaagactaacaacttttatagattatatttatgtagaccgtacacttatgttcataagactcacgttactttgttggttgaaaaatgaaaagGTGGAGCAGAGATATAGACAGTACCACCAGCAGATGCAGATGGTGATCTCTTCGTTCGAGCAAGCGGCAGGGATAGGATCAGCGAAGTCATACACGTCGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35940.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g06020.1 (Oryza sativa), 3'ss of exon 2
ctcttagtaaagactaacaacttttatagattatatttatgtagaccgtacacttatgttcataagactcacgttactttgttggttgaa--aaatgaaa---agGTGGAGCAGAGATATAGACAGTACCACCAGCAGATGCAGATGGTGATCTCTTCGTTCGAGCAAGCGGCAGGGATAGGATCAGCGAAGTCATACACGTCGC
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----aatcatcagctagctg-ttgtacagtgagtagctatctactccaattaattaagcacaatcaactaatgaatctccatggatgggatgggatgggatgcagGTGGAGCAGCGGTACAGGCAGTACCACCAGCAGATGCAGGTGGTGGTGGCGTCGTTCGAGGCGGTGGCGGGGGGCGGGTCGGCGAGGACGTACACGGCGC
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 3
ctcttagtaaag-actaacaacttttatagattatattta---tgtagaccgtacacttatgttcataagactcacgttactttgttg-gttgaaaaatgaaaagGTGGAGCAGAGATATAGACAGTACCACCAGCAGATGCAGATGGTGATCTCTTCGTTCGAGCAAGCGGCAGGGATAGGATCAGCGAAGTCATACACGTCGC
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---aaggtcatgtattatataattttataatatagtcctactttgtagtagcattattttgtttcttgatttctaatttacatgattttgtttgggattgaa--gGTGGAGCAAAGGTACAGGCAGTACCACAGCCAGATGCAGATTGTGATATCCTCTTTCGAGCAAGCTGCTGGGATAGGCTCAGCGAGGACGTACACTGCTC
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G38690.1 (Glycine max), 3'ss of exon 5
-------ctcttagtaaagactaacaacttttatagattatatttatgtagaccgtacacttatgttcataagactcacgttactttgttggttgaaaaatgaaaagGTGGAGCAGAGATATAGACAGTACCACCAGCAGATGCAGATGGTGATCTCTTCGTTCGAGCAAGCGGCAGGGATAGGATCAGCGAAGTCATACACGTCGC
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cttaaattgcatggttgtggttgattgcagtta-ataaaatatttgtgaagt---tgaattaatggatagtttattgatgtgattctatttttcttt---cttgaagGTGGAGCAAAGGTACAGGCAGTACCAGCAGCAGATGGAGATAGTGGTTTCATCGTTTGAGCAAGCTGCGGGGATTGGTTCTGCGAGGACTTACACTGCCC
upper sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 9
ctcttagtaaagactaacaacttttatagattatatttatgtagaccgtacacttatgttcataagactcacgttactttgttggttgaaa-aatgaaaagGTGGAGCAGAGATATAGACAGTACCACCAGCAGATGCAGATGGTGATCTCTTCGTTCGAGCAAGCGGCAGGGATAGGATCAGCGAAGTCATACACGTCGC
| | || || | || || ||| | || || | | | || | | | || || || ||| | ||||||||||| ||||| | ||||| || || ||||||||||| ||||| ||||| |||||||||||||||||||| || || || || | ||||| | |
aaaattgaaatttctgaggacaggtacagagtgctttgtaatatcatggcagcatgtgaaactgtaaattgacttgctc-attatttgtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgtacacttatgttcataagactcacgttactttgttggttgaaaaatgaaaagGTGGAGCAGAGATATAGACAGTACCACCAGCAGATGCAGATGGTGATCTCTTCGTTCGAGCAAGCGGCAGGGATAGGATCAGCGAAGTCATACACGTCGC
gactcac putative branch site (score: 2)
ttgaaaaatgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcttagtaaagactaacaacttttatagattatatttatgtagaccgtacacttatgttcataagactcacgttactttgttggttgaaaaatgaaaagGTGGAGCAGAGATATAGACAGTACCACCAGCAGATGCAGATGGTGATCTCTTCGTTCGAGCAAGCGGCAGGGATAGGATCAGCGAAGTCATACACGTCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG