Sequence
atgc intronic sequence ATGC exonic sequencegtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaataactccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46340.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 8
gtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaataactccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
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----gtaaggtat---atatctacgca--tcccattgccattttaaatcatggatca-agagtt-gaaga--ttggaaacaaatg-atcttttttgttcagGTTACAAAAACCCA--GAGCCTTCTAAGATGAACTTACCCCTGTTACACGAATGGCGCTTCCGCTCTGGCCTTGATCGTTACATATGGATCATTGGAATGAT------
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
gtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaata-actccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
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-------gcttttgt-atgttgtctg--tttgcaattttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
gtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaata-actccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
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-------gctttt--gtatgtagtctgtttgcaattttctagttgatttgctaata-taagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 3
gtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaataactccagGTTACAATGACCCTG------CCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
||| ||| ||| | | ||| || | | || ||| | | | | | ||| |||| | ||| | | || | | || ||||||||| ||| || | | || | | ||| | ||| |||||||||||||| |||||||| || ||||||||||| || |||||||||||||||||
---attactatatt-gaactggtttg--ttgcta--gttcaatctagtggcttaacaccaagttaagttgtgttttccaagttttcaaactagt-attttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT------
upper sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S357_34V6.1 (Physcomitrella patens), 3'ss of exon 8
---gtggttagcttatccgaaattgattg-aattcccaatgtggaatgagattattcataatggaattagaagaagtttctaa-tatttgtatattacttgtgaataactccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
| ||| | | | || |||| || | ||| | || ||| | |||| ||| |||| || | ||||| || ||| || || | | | | || | |||| | || |||||||||||||||||| |||||||| || ||||| ||||| ||||| | || ||| | ||
ggactagtt-gtgcaccattcataaattgtgatccttaatttcatggcagtttaatgataac----ctagcgatagttgctgagtatttttac-ttatttttg-----cagCGTATCAAGATCCTTTATCAAAGCACCCCACTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatggaattagaagaagtttctaatatttgtatattacttgtgaataactccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
gaataac putative branch site (score: 2)
taatatttgtatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaataactccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA