Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcttgtttttgctcatttttctaagtttgtcttgaacatatggtaagattgctgcaggattattgtttttgcagATATCATTACCAGCTTCCTTCTGGTCAGCCAAATCATACTTGTGGTGGAGCTGATATTTGGGCTGATATTGGTAGTAGTAGTGAAGTTTTCTGTTCAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60740.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G20220.1 (Glycine max), 3'ss of exon 2
gtaagtcttgtttttgct------catttttctaagttt-gtcttgaacatatggtaagattg--ctgcaggattattgtttttgcagATATCATTACCAGCTTCCTTCTGGTCAGCCAAATCATACTTGTGGTGGAGCTGATATTTGGGCTGATATTGGTAGTAGTAGTGAAGTTTTCTGTTCAGCT
||||||| | | | | ||| |||||| ||| || || || | ||| ||| | ||| || | | | ||||||||| ||| ||||||||| |||| |||| || |||||||||||||| || ||||||||||| |||||| ||||||||||| || |||||||||||
gtaagtcctttcccttttaagttatattgttctaatttttgtttttggcacactttaatatttatcaacagaatcaatat----gcagATATCGTTATCAGCTTCCTCCTGGAAAGCCTAACCATACTTGTGGTGGGGCAGATATTTGGGCAGATATTCAGAGTAGTAGTGAGGTGTTCTGTTCAGCA
upper sequence: AT5G60740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G08290.1 (Glycine max), 3'ss of exon 2
gtaagtcttgttttt----gct-catttttctaagt--ttgtcttgaacatatggtaagattg--ctgcaggattattgtttttgcagATATCATTACCAGCTTCCTTCTGGTCAGCCAAATCATACTTGTGGTGGAGCTGATATTTGGGCTGATATTGGTAGTAGTAGTGAAGTTTTCTGTTCAGCT
||||||| | || | | ||| ||||| | |||| || || | ||| ||| | ||| || | | | ||||||||| ||| ||||||||| |||| |||| || |||||||||||||| || ||||||||||| |||||| |||||
gtaagtccttcccttttaagttatattgttctacattcttgtttttggcacactttaatatttatcaacagaatcaatat----gcagATATCGTTATCAGCTTCCTCCTGGAAAGCCTAACCATACTTGTGGTGGGGCAGATATTTGGGCAGATATTCAGAGTAGCG--------------------
upper sequence: AT5G60740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g02490.t01 (Vitis vinifera), 3'ss of exon 4
-------gtaagtcttgtttttgctcattt-ttctaagtttg---tcttgaacatatggtaagattgctgcaggattattgtttttgcagATATCATTACCAGCTTCCTTCTGGTCAGCCAAATCATACTTGTGGTGGAGCTGATATTTGGGCTGATATTGGTAGTAGTAGTGAAGTTTTCTGTTCAGCT
| ||||| || | |||| || || |||| ||||| || ||| || | || || | ||||| || ||||||| || ||| | || |||| |||| | ||||||||||||||||||||||||||||||||| |||||||| || | |||||||||||
gtaagtttagattcttgattggaattatttcttttatgtttaatttcttgtgtttagcataatataattaacagaaaat---gtatgcagTTACAATTACCAACTACCTCCAGGGCAGCAAAATAGAAGTTGTGGTGGAGCTGATATTTGGGCTGATATTGGGAGTAGTAGCGAGATATTCTGTTCAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaagtttgtcttgaacatatggtaagattgctgcaggattattgtttttgcagATATCATTACCAGCTTCCTTCTGGTCAGCCAAATCATACTTGTGGTGGAGCTGATATTTGGGCTGATATTGGTAGTAGTAGTGAAGTTTTCTGTTCAGCT
ttgttttt CT-rich tract
attattgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcttgtttttgctcatttttctaagtttgtcttgaacatatggtaagattgctgcaggattattgtttttgcagATATCATTACCAGCTTCCTTCTGGTCAGCCAAATCATACTTGTGGTGGAGCTGATATTTGGGCTGATATTGGTAGTAGTAGTGAAGTTTTCTGTTCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT