Sequence
atgc intronic sequence ATGC exonic sequencegtactactactaatgaaataagattggtgtttttttgtttgagagatttggactgttgttgtgtgaagatttgattttcttttgggttttcaaatgtttagGCAAGAAAGCCATATACAATAACAAAGCAGCGAGAGCGATGGACTGAGGATGAGCATGAGAGGTTTCTAGAAGCCTTGAGGCTTTATGGAAGAGCTTGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01060.5 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01060.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G45030.1 (Glycine max), 3'ss of exon 1
gtactactactaatgaaataag-attggtgtttttttgtttgagagatttggactgttgttgtgtgaagatttgattttcttttgggt-----tttcaaatgtttagGCAAGAAAGCCATATACAATAACAAAGCAGCGAGAGCGATGGACTGAGGATGAGCATGAGAGGTTTCTAGAAGCCTTGAGGCTTTATGGAAGAGCTTGGC
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-----tgtaaagtggaaacaactatataggccaaaatattaaataaacctt-attattattgt-tgttatttttattattatctgagtggctacttggcaattgtagACAAGAAAGCCATATACTATCACAAAGCAAAGAGAACGATGGACAGAGGAGGAACATAACAGATTTCTAGAAGCCTTGAAGCTATACGGGCGAGCATGGC
upper sequence: AT1G01060.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G42260.2 (Glycine max), 3'ss of exon 3
gtactactactaatgaaataagattggtgtttttttgtttgagagatttggactgttgttgtgtgaagatttg--attttcttttgggttttcaaatg-----tttagGCAAGAAAGCCATATACAATAACAAAGCAGCGAGAGCGATGGACTGAGGATGAGCATGAGAGGTTTCTAGAAGCCTTGAGGCTTTATGGAAGAGCTTGGC
|||| | || | || | | | | | || || ||| |||| || || | | || | || ||||||| |||||||| || |||||||| |||| |||||||| ||||| || ||| | || |||||||||||||||| ||| || || |||| ||||
-----------------gtaagtactttattgtggtggattaatggcaaacttcgataccccaaagggaattattattatcttctgagtggttacttggcaattgcagACAAGAAAACCATATACTATCACAAAGCAAAGAGAACGATGGACAGAGGAGGAACATAACAGATTTCTAGAAGCCTTGAAGCTATACGGGCGAGCATGGC
upper sequence: AT1G01060.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G01980.4 (Glycine max), 3'ss of exon 2
---------gtactactactaatgaaataagattggtgtttttttgtttgagagatttgg-actgttgttgtgtgaagatttgattttcttttgggttttcaaatgtttagGCAAGAAAGCCATATACAATAACAAAGCAGCGAGAGCGATGGACTGAGGATGAGCATGAGAGGTTTCTAGAAGCCTTGAGGCTTTATGGAAGAGCTTGGC
| | || ||| ||| || ||| | || || || || | | ||| | || | |||| || || || || | ||||| ||||||||||| || ||||| | || |||||||| ||||| |||||| | |||||||||||||| |||| || | || |||| ||||
gttagagttattgtgatatatatgggg-aagtttctcactttctcgtgaaagtgagttagtaaagttttggtactgttgtctgatgagtggttaagtggctttttgc--agACTAGAAAACCATATACAATCACTAAGCAAAGGGAACGATGGACAGAGGAGGAGCATAATAGGTTTCTAGAAGCTTTGAAACTACACGGGCGAGCATGGC
upper sequence: AT1G01060.5 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0048g02410.t01 (Vitis vinifera), 3'ss of exon 1
gtactactactaatgaaataagattggtgtttttttgtttgag---agatttggactgttgttgtgtgaagatttga---ttttcttttgggttttcaaatgt----------------------ttagGCAAGAAAGCCATATACAATAACAAAGCAGCGAGAGCGATGGACTGAGGATGAGCATGAGAGGTTTCTAGAAGCCTTGAGGCTTTATGGAAGAGCTTGGC
|| | ||| | ||||| || | ||||| ||| | | | | || | ||| | || |||| | || ||||| | |||||| | || |||| || || ||||| || || |||||||| ||||||||||| ||||| |||||| | |||||||| || ||||||| ||||||||| |||||||||
gtgattttacataggaaatttttttatttatttttcttttatgctgaattcttgaatcagtctgtacaatgacttgaaactattgttttgacgatgaaaatgtgagttatgaatcttggtcaacatcagACAAGGAAACCGTATACTATTACCAAGCAGCGGGAGCGATGGACAGAGGAGGAGCATAATAGGTTTCTGGAGGCCTTGAAGCTTTATGGGCGAGCTTGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggactgttgttgtgtgaagatttgattttcttttgggttttcaaatgtttagGCAAGAAAGCCATATACAATAACAAAGCAGCGAGAGCGATGGACTGAGGATGAGCATGAGAGGTTTCTAGAAGCCTTGAGGCTTTATGGAAGAGCTTGGC
atttgat putative branch site (score: 5)
atttgattttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactactactaatgaaataagattggtgtttttttgtttgagagatttggactgttgttgtgtgaagatttgattttcttttgggttttcaaatgtttagGCAAGAAAGCCATATACAATAACAAAGCAGCGAGAGCGATGGACTGAGGATGAGCATGAGAGGTTTCTAGAAGCCTTGAGGCTTTATGGAAGAGCTTGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT