Sequence
atgc intronic sequence ATGC exonic sequence...tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
Basic information
| species | Arabidopsis thaliana |
| transcript | AT2G30460.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
---tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaactt-acagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
||| | || | || | | | ||| | ||| | | || | | |||| ||| | | | |||| || || |||| ||||||||||||||||||||||| | || |||||||| || ||||| ||||||||||| |||||| | ||||||||||| ||||||||| || | |
ggttctaaagtgtgtgacaatactaggtaacgtaaaaagtta-gtacataaatagacgtgtttcctgtcca-aattactca--acttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 2
----tctttaccatgggt-gaactccattcatgataacagtttatgcatggaatctcatagt-ctatctgtgtgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
| | | ||| | | | | ||| || | || | | |||| | || | | |||| | | ||| || || |||| || |||| ||||| ||||| || ||||||||| | || |||||||| || || ||||| ||||||||||||||||| || |||||||||||||| || | || |
ttcttttctcaaatgcattgcaatgtattagtgtttgtagaatttacatgaatataaatgacaccaactgttttt--ccatacatggaattgtatt----ttgcagCCACTACCTTGACGAGTTGGCATCTTCTTGTCACATTTTGCTCCCTCCATGTAGCATTATGGATGAAGTTCTTCGAGCACAAGCCTTTCGACTCGAGAAC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g60780.2 (Oryza sativa), 3'ss of exon 1
tctttaccatgggtg-aactccattcatgataacagtttatgcatggaa---tctcatagtctatctg--tgtgtaatcatt-tattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
||| || || | | ||| || | | | || | || || |||| | || || || | ||| | ||| |||| ||||| |||||||||||||||| |||||||||||||||| ||||||||||| | ||||||| |||| ||| |||| ||| || || |
-------tatgagtacaatatgacgaacaataccacctgagaaaactaactgtttcctaagctatataaccatgcaaaaatcacagcactctcctaatttctttcagCTACTACGCTGACAAGCTGGCATCTCCTGGTGACATTTTGTTCCCTTCATGTGGCTCTTCAGATGAAGCTTTTCGAGAACAAAGATTTAGACCCCAAGAC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 2
tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaactt--acagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
|| | || | || | ||| | | || | | |||| | || || || | | | |||| ||| |||| ||||| ||||||||||||||||| |||| ||||| || || ||||||||||||||||||||||| || |||||||| |||||||||||| || || |
-acacgccccttattttatcaacatgtggtgg-agtatgcaagtctgatttaaatgtcttcttatggactatggttgtgaaatatgtatttgtcttctgcagCCACTACCTTGACAAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTGGCATTATGGATGAAATTCTTTGAGCATAAGCCTTTTGATTCAAGAAC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 2
tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttatta--ctttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
| || | || | ||||| | ||| | || | | | | | || || || | | |||| | || |||| ||||||||||||||||||||||| |||| ||||| ||||| || |||||||||||||| |||||| | ||||||||||| ||||| ||| || | |
caagtgtggtgaggtgacagtgcgtctataaacagataatgatagcaaag--aaggcaggttttcctccaagtgttaataaaatgtggtattcattttgcagCCACTACTTTGACAAGCTGGCATCTCCTGGTTACATTCTGTTCTCTCCATGTGGCATTATGTATGAAGCTGTTTGAGCACAAACCTTTCGATGCAAGGAC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 1
------tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
|| | | | | | | ||| ||| || |||| | | ||| || | | | |||| | | | | ||| || |||| ||||| ||||| ||||||||||| |||| ||||| || || |||||||| ||||||||||||||||| |||||||| |||||||||||| || || |
cagagtactagatcttatattatcaacatgtatg-tagtgaagtatgta---agtctgat--ttaaatgacttctaatatctgtgaaatatgtatgtcttttgcagCCACTACCTTGACGAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTAGCATTATGGATGAAGTTCTTTGAGCATAAGCCTTTTGATTCAAGAAC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 1
tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactt-tatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
|| | | | ||| || | | || || | | || | | | | | ||| || |||| ||||| ||||| ||||||||||| |||| ||||| || || |||||||| ||||||||||||||||| |||||||| |||||||||||| || || |
----------------------------gtatgtagtgaagtatgtaagtc--tgatttaaatgacttctaatatctgtgaaatatgtatgtcttttgcagCCACTACCTTGACGAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTAGCATTATGGATGAAGTTCTTTGAGCATAAGCCTTTTGATTCAAGAAC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 2
-tctttaccatgggtga-actccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
| | || |||| | ||| | || | | | ||| | || | || | | | || | | | |||| | || |||| || ||||||||||||||||||||| |||| || || || || || ||||| |||||||| ||||| | ||||||||||| ||||| ||| || | |
cacgtgtcctcaagtgacagtccgtctataaacagataatattagcaaagaaggcaggttttcctccatatgctaataaa--atctcgtattcattttgcagCCACCACTTTGACAAGCTGGCATCTTCTGGTCACCTTCTGCTCTCTCCATGTAGCATTATGTATGAAACTCTTTGAGCACAAACCTTTCGATGCAAGGAC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
---tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
||| | || | |||||| | || | || || | | | || ||| || | | | | || | | | | | |||| || ||||||||||| ||||||||| | || ||||||||||| |||||||||||| || | ||| ||||||||||||| |||||||| | |||
taacttttgttagaagt-agctccatgctgcatcctaacccatt--tgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 2
tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttatt--actttata---ttgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
| || ||||| | ||| | | || ||| | | | | || || |||| | | | | || || | ||| | || | | |||| || |||||||| ||||||||||| | || ||||||||||| ||||||||||| | |||| || ||||||||||| |||||||| | |||
ttatttccatgatatatgcaaatttgagct-----ttcatgtttacattttaatgtactgtctgagatttacaagtttttgaaatttgtgctttttgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACATTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
tctttaccatgggtgaactccattcatgataacagtttatgcatgg--aatctcatagtctatctgtgtgtaatcattt--attactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
| | |||||||||| | | | || | | | || | || || || |||||| | ||| | | | || |||| || ||||| || |||||||||||| |||| ||||||||||| |||||||||||| |||||||||| || |||||||||||||||||||| | ||||
---agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtcttgagttctcattttaactacccaactgtcga-ttgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC
upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
---tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtg-tgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
| | | | | | | || || | || || || | |||| |||| | ||| | | | | ||| |||||| ||||| |||||||||||||||||| |||| || || ||||| ||||||||||| |||||||||| || ||||| ||||| || |||||| || |||
gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttg----tacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatctcatagtctatctgtgtgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
taatcatttattactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC
- - - - - - - -aactcca
- - - - - - - - - - - - - -gataaca
- - - - - - - - - - - - - - - - - - - - - - - aatctca
