Sequence
atgc intronic sequence ATGC exonic sequencegtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattgcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G03000.1 |
| intron # | 9 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os04g52690.1 (Oryza sativa), 3'ss of exon 10
gtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttct-tcaattgcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
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gtaaattg-atttacacaaccatacaattgccataagatgtgcatat-----atgcttacggttgcaactcttctgtcaacctcagGCAAGATCTGCACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAG
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G445617_T01 (Zea mays), 3'ss of exon 10
----gtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattgcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
|| ||| | | | | | ||| | | ||| ||| || | | | || ||| ||||| ||||| ||||| || || || ||||| || |||||||||||||||||||| |||||||| || ||||| | || | |||||||| || |||||||| | |
gtacagaatttacacagccatgtaattgtgtgaaacgtgcatagttttt--ttttcagttttccactg-----------tcaatctcagGCTAGGTCTGCACGCCCATGTGTCATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCAGCAGATTCTGGCGGTGTCATGGACAGGG
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 10
------------------------------------------------gtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttcttcaatt-gcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
|||| | | ||| | | | || | | || ||| || | | |||| | | | | || |||| ||||| || ||||| || || ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||| |||||||| || || ||||| |||
gtataataatattccggatttttttatctaaataatttctcaatttgagtaaat-gtgtttgtgcctttttactgtgaac-taaacagttttcagaacagattttgataaaatgaacttcaaaataattcacagGCCAGATCAGCACGTCCATGTGTCATCTTCTTTGATGAGCTTGATTCTCTTGCACCAGCTCGAGGTGCCTCTGGAGATTCTGGGGGTGTTATGGACAGAG
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G36930.1 (Glycine max), 3'ss of exon 15
------------------------------------------------gtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttct--tcaattgcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
| | | ||||| | || | | | | ||| ||| | | |||| | | | | || || | | | ||||| || ||||| | || ||||| ||||||||||||||| ||||||||||||| |||||||| ||||||||||| |||||||| | || ||||| |||
gtataataatatttcagtttcttttatctaaataatttctcaagttaaattaaatgtatttgtgtctctttgctgtgaactcaac-agtttttagaacagattttgatccaaatgaaattcaaaataattcacagGCCAGATCAGCATGTCCATGTGTCATCTTCTTTGATGAGTTTGATTCTCTTGCACCAGCTCGGGGTGCTTCTGGAGATTCTGGGAGCGTTATGGACAGAG
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 10
gtaagttatatttcttcttccctaggagaagcatattgagtct--ttggttctgatt---cttaaactagtgtgtttt----cttcaattgcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
|||| ||||| | | ||| | || ||| ||| || || || | | | |||| | | || ||| ||||||||||||| || || ||||| |||||||||||||| |||||||||||||||||||| |||||||| ||||| |||||||| || || ||||| |||
gtaaag-atattcttatgtgattagaatgccttgttttgctctaacatgttttggttgacctcacaattctgtgacattgggcatcctttgtagGCAAGGTCAGCACGTCCATGTGTTATCTTCTTTGATGAACTTGATTCTCTTGCTCCAGCCCGAGGTGCCTCTGGGGATTCTGGGGGTGTTATGGACAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattgcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
ttctgat putative branch site (score: 3)
tgttttcttc putative PPT
attcttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattgcagGCAAGGTCAGCGCGACCTTGTGTGATCTTCTTTGATGAGCTTGATTCTCTTGCTCCAGCTCGAGGTGCTTCTGGTGATTCTGGAGGAGTCATGGATCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
