Sequence
atgc intronic sequence ATGC exonic sequencegtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTTTAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01320.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTT-TAAATC-TATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG------------------------
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------------tcactagtt-ttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 16
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTTTAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG--------------------------
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----------------------------------------------------------------------------------------------gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 16
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTTTAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG------------------------
||||| |||||||| | || | | || || | | | | | | |||| | | | |||| || | | || | | | |||||||||||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||||||||| ||||||||||
gtaacaaacaagaca-tgttgatcataggttttcttgcatatttctttgaagttgattgaataaatc------caaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 1
gtaacggacaagacaatagatatta-ggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccat--agttattcagACTT---TCTATTT-TAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG------------------------
|| | | |||| | || | | ||| ||| | | | || | ||| | | | | | | |||| | | || || || | |||| | ||| | |||||||||||||| |||||||| |||||| | |||||||| || ||||| |||||| || |||| || ||||| ||||
gtgatgaacaaactatgctatttgatagaagaatagaacacattgtttcttatcttgtcttacaaataattaaaccattcaataatctggatttaattgcatttctttttcttttcagCAAGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAACTATAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAA
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 16
gtaacggacaagacaatagatatta-ggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccat--agttattcagACTT---TCTATTT-TAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG------------------------
|| | | |||| | || | | ||| ||| | | | || | ||| | | | | | | |||| | | || || || | |||| | ||| | |||||||||||||| |||||||| |||||| | |||||||| || ||||| ||||||||| |||| || ||||| ||||
gtgatgaacaaactatgctatttgatagaataatagaacacattgtttcttatcttgtcttacaaataattaaaccattcaataatctggatttaattgcatttctttttcttttcagCAAGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAGCTCTAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTTTAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG
ttctaat putative branch site (score: 2)
attctttctaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTTTAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA