Sequence
atgc intronic sequence ATGC exonic sequencegtaggatcactggctcttttatcctttagttagacagttgattgaatatatatgtttctttttgtatgactctcattcaaatgttgtagAACTTGGCAAATAGACAAAAACCTGGATGTGCAAAAGGATCTGGTGTGGATCGATCAAGAACAGCAACAACACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08080.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08080.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g07000.1 (Oryza sativa), 3'ss of exon 5
----------gtaggat-cactg-gctcttttatcctttagttagacagttgattgaatatatatgtttctttttgtatgactctcattcaaatgttgtagAACTTGGCAAATAGACAAAAACCTGGATGTGCAAAAGGATCTGGTGTGGATCGATCAAGAACAGCAACAACACT
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aggatttgctatacttttcactaagccatctcacgtgctagtgtcatttgtcaatagcaacattgagttgtctct-cactgttcgctgccatgtgaaacagAACTTATCAAACAGACAAAAGCCTGGATGTGGGAAAGGATCTGCGGTAGATCGATCAAGAGAACAGACTACTGG
upper sequence: AT5G08080.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G330772_T01 (Zea mays), 3'ss of exon 5
------------gtagg-atcactggctcttttatcctttagttagacagttgattgaatatatatgtttctttttgtatgactctcattcaa-atgttgtagAACTTGGCAAATAGACAAAAACCTGGATGTGCAAAAGGATCTGGTGTGGATCGATCAAGAACAGCAACAACACT--
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agaacttatgaaataggtatctataattgtttaaatcg--agctgacttgtgcgctgc-tatcaacaattaaccttgaattgttcgctaccattatggtacagAACTTATCAAATAGGCAAAAACCTGGATGTGGAAAAGGTTCTGCCGTGGACCGATCAAGAG-AGCAA-ACTACTGG
upper sequence: AT5G08080.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G27050.1 (Glycine max), 3'ss of exon 5
gtaggatcactggctcttttatcctttagttagacagttgattgaatatatatgtttctttttgtatgact-ctcattcaa----atgttgtagAACTTGGCAAATAGACAAAAACCTGGATGTGCAAAAGGATCTGGTGTGGATCGATCAAGAACAGCAACAACACT
|| || | | | ||| | ||| || ||| | ||||| |||| | ||||||| | | |||||||| |||||||| || || || ||||| |||| ||||||||| ||||| || || ||||||||||| ||||| |
---------gtgactttactgaatgcca-ttaattgtcttattcaacccata-gattcttggtgtaaatcgactcattccattctgtattgtagAATTTGGCAAACAGGCAGAAGCCTGGGTGTGGAAAAGGATCAGGTGTTGACCGGTCAAGAACAGCGACAACCAT
upper sequence: AT5G08080.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0032g00440.t01 (Vitis vinifera), 3'ss of exon 5
gtaggatcactggctcttttatcc--tttagttagacagttgattgaatatatatgtttctttttgtatgactctcattcaaatgttgtagAACTTGGCAAATAGACAAAAACCTGGATGTGCAAAAGGATCTGGTGTGGATCGATCAAGAACAGCAACAACACT
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gtaagactatttgttgctgctttgagttcattctaacaatt--ttcagttcttggagttcttgtttgaccataactttttgtg-gccccagAATTTAGCCAATAGGCAGAAGCCTGGATGTGGAAAAGGAACAGGTGTAGATCGATCAAGAACTGCAACAACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttgattgaatatatatgtttctttttgtatgactctcattcaaatgttgtagAACTTGGCAAATAGACAAAAACCTGGATGTGCAAAAGGATCTGGTGTGGATCGATCAAGAACAGCAACAACACT
agttgat putative branch site (score: 5)
attgaatatatatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggatcactggctcttttatcctttagttagacagttgattgaatatatatgtttctttttgtatgactctcattcaaatgttgtagAACTTGGCAAATAGACAAAAACCTGGATGTGCAAAAGGATCTGGTGTGGATCGATCAAGAACAGCAACAACACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC