Sequence
atgc intronic sequence ATGC exonic sequence...cttctcggattgaacattttagtttcaaatgattgtaataatttgtggcacatttctgtggttagcaatatttctttctgacccaatgtttttgttttagGTTGGGAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
cttctcggattgaacattttagt-ttcaaatgattgtaataatttgtggcacatttctgtggttagcaatatttctttctgacccaatgtttttgttttagGTTGGGAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATG
| | | || | | |||| | | || |||| | || | | | | | || || | || || | | ||||||| || ||||| ||||| ||||||||||||||||| ||||| ||| | ||||| ||||| || || |||||||| ||||||||||| || || ||||
gaaaccaaacaacattttctgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgt-agGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 5
---cttctcggattga--acattttagtttcaaatgattgtaataatttgtggcacatttctgtggttagcaatatttctttctgacccaatgtttttgttttagGTTGGGAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATG
|||| | || || | | || || | | ||| | || | | | | | | |||| | ||| | | || | ||||||||| ||| | || ||||| ||||| || || || |||||||| ||| | ||||| || ||||| |||||||| |||||||||||||| || || ||||
taatttctggttttcctttcactcttattagttatattactgatagtctgatgtataactaatcaacttg--atatctgttttgggtattacatt---atcttagGTTGGCAATAGGTCCAGTGAATTTCACCCAGAAGTGAGAAGAGTGAGGCGTGAAGGATCCTATATTTATGAGGAATTTATGCCTACTGGAGGGACAGATG
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 7
------cttctcggattgaacattttagtttcaaatgattgtaataatttgtggcacatttctgtggttagcaatatttctttctgacccaatgtttttgttttagGTTGGGAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATG
|| | | || ||||| || ||||| |||| || | | | |||| || ||| || | | | | || |||||| ||||||| || || ||||||||||| ||||| || || |||||||| ||| | ||||| ||||||||||||||||| |||||||| ||||| ||||| ||||
cactagatttttagcttc--tattttcattgtaaatgtttgt--ccatacatcttatacttcttccgtgtgca-tacacacatataatttt-tattattgtttcagGTTGGTAACCGCTCAAGTGAGTTCCATCCAGAGGTTAGAAGAGTGAGGCGTGAAGGCTCTTATATATATGAGGAATTTATGCCAACTGGAGGAACAGATG
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 7
cttctcggattgaacattttagtttcaaatgattgtaataatttgtggcacatttctgtggttagcaatatttc-tttctgacccaatgtttt--tgttttagGTTGGGAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATG
| | | ||||| || | ||| |||| |||| || || || |||| ||||| ||||||||||||||||| || | ||| |||| | |||||||| |||||||| ||||||||||||||||| ||||||||||| ||||
-------------------------------------------------gtgatgaagcattaagcaaaatgtaacctcttacccgatgtattaatgccgcagATTGGAAATCGTTCAAGTGAGTTTCATCCCGAGATAAGACGAGTTCGAAGAGAAGGCTCTTATATCTATGAGGAGTTTATGCCAACTGGGGGAACAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggcacatttctgtggttagcaatatttctttctgacccaatgtttttgttttagGTTGGGAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATG
ttctgac putative branch site (score: 2)
tttttgtttt putative PPT
aatgtttttgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttctcggattgaacattttagtttcaaatgattgtaataatttgtggcacatttctgtggttagcaatatttctttctgacccaatgtttttgttttagGTTGGGAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG