Sequence
atgc intronic sequence ATGC exonic sequencegtatgattataagctgtcttatttgtttttttactcttgaagatttgtggttttagagtttgatgttctctgttgttacagGCAAGAGAAGGCAAAAGCAGTTGAGATACTAGTGCAAGATTTGAGAGTTTTCTCCACTTTCAATGAGGAGCTTTACAAAGAAATCACTCAACTCTTAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27030.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 2
--------------gtatgattataagctgtcttatttgtttttttactcttgaagatt-------tgtggttttagagtttgatgttctctgttgttacagGCAAGAGAAGGCAAAAGCAGTTGAGATACTAGTGCAAGATTTGAGAGTTTTCTCCACTTTCAATGAGGAGCTTTACAAAGAAATCACTCAACTCTTAACT
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gtatctattaatttgaatctcttttggattttctaattttgtttgtgcttatgatggtacttcacatgttgtttttgtctttggtgctgttaaatttta--gGCAAGACAAGGCAAAGGCTGTTGAGATATTAGTGGGTGATTTAAAAGTTTTCTCCACCTTCAATGAGGAACTATACAAAGAAATCACCCAGCTGTTAACT
upper sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 3
--------------gtatgattataagctgtcttatttgtttttttactcttgaagat---ttgtggttttagagtttgatgttctctgttgttacagGCAAGAGAAGGCAAAAGCAGTTGAGATACTAGTGCAAGATTTGAGAGTTTTCTCCACTTTCAATGAGGAGCTTTACAAAGAAATCACTCAACTCTTAACT
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gtatctattaatttgaatctatttgggattttctaattgtttttgtgcttatggtggtacttcacatgttttatctttggtgctcttc--tattttagGCAAGACAAAGCAAAGGCTGTTGAGATATTGGTGGGTGATTTAAAAGTTTTCTCCACCTTCAATGAGGAACTATACAAAGAAATCACCCAGCTGTTAACT
upper sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 2
--------------gtatgattataagctgtcttattt--gtttttttactcttg-----aagatttgtggt-tttagagtttgatgttctctgttgttacagGCAAGAGAAGGCAAAAGCAGTTGAGATACTAGTGCAAGATTTGAGAGTTTTCTCCACTTTCAATGAGGAGCTTTACAAAGAAATCACTCAACTCTTAACT
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gtatgcggaactttgttatctttttaactattttttctaaacatgtttgcgcttgttatgaaatttcacattgttttgtctctggtgtttttcaa-attttagGCAAGACAAGGCAAAGGCCGTGGAGATATTAGTGGGTGATTTGAAAATGTTCTCCACCTTCAATGAGGAGCTATACAAAGAAATAACCCAGTTATTAACT
upper sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 2
-----gtatgattataagctgtcttatttgtttttttactcttgaagatttgtggtt--ttagagtttgatgttctctgttgttacagGCAAGAGAAGGCAAAAGCAGTTGAGATACTAGTGCAAGATTTGAGAGTTTTCTCCACTTTCAATGAGGAGCTTTACAAAGAAATCACTCAACTCTTAACT
| || | || | | | || | | ||| | |||| || ||| || || | || | ||||||||| |||||||| || || |||||| ||||| |||||| || || ||||| ||||||||||| || | || |||||||||||||| || || ||
gtaaattttgtatctatattttggaagttctgtgtttgtatcaggagatactaaattgattaagtaatggagtgttgatttatctcagGCAAGACAAGGCAAAGGCTGTAGAGATATTAGTGACAGATTTAAGGGTGTTCTCAACTTTCAATGAAGACTTGTATAAAGAAATCACTCAGCTTTTGACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttactcttgaagatttgtggttttagagtttgatgttctctgttgttacagGCAAGAGAAGGCAAAAGCAGTTGAGATACTAGTGCAAGATTTGAGAGTTTTCTCCACTTTCAATGAGGAGCTTTACAAAGAAATCACTCAACTCTTAACT
gtttgat putative branch site (score: 5)
ttctctgtt CT-rich tract
aagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattataagctgtcttatttgtttttttactcttgaagatttgtggttttagagtttgatgttctctgttgttacagGCAAGAGAAGGCAAAAGCAGTTGAGATACTAGTGCAAGATTTGAGAGTTTTCTCCACTTTCAATGAGGAGCTTTACAAAGAAATCACTCAACTCTTAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA