Sequence
atgc intronic sequence ATGC exonic sequence...agtttcaggttcacattgttgatatttacttgagctgaagaatcaattttctgtttcacattgttgatgtttggttgttggtgtgcattggtaataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55120.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G43200.1 (Glycine max), 3'ss of exon 4
---agtttcaggttcacattg---ttgatatttacttgagctgaagaatcaattttct--gtttcacattgttgatgtttggttgttggtgtgcattggtaataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
| || || | |||| ||||| | || || | |||||| | || ||| | | |||||| | || | || |||| || ||| || || |||||||| ||||||||||| ||||||||||| ||||| || ||||||||||||||||| |||||||||||||| || || || ||||| |
gtctgatttgtgtacccatttggtttgattcactttctagttgtgattttggttttcttgggtttgcatggatattgtttgatg--tgttttgttttgggttta---gGTGATTCCTGGGAAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGCCACCTCAAGAAGAGACCAACTGAGTTCCGTGTTGATAAGGTCCTCCAACCCT
upper sequence: AT5G55120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G10430.1 (Glycine max), 3'ss of exon 3
agtttcaggttcacattgttgatatttacttgagctgaagaatcaattttctgtttcacat-tgttg--atgtttggttgttggtgtgcattggt--aataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
|| | | | || | ||| || | || | | ||| ||||| | | |||| ||| || | ||| |||| ||| | ||||| || || ||| |||| ||||||||||| ||||||||||| ||||| || ||||||||||||||||| ||||| |||||||| || || || || ||
ggtctgatttatgtatccatttagtttgattca-ctttctagttgtgtttttgttttgcttgtgtttgcatggatgttgtttgatgtgttttgttttgggtttaGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTTCGTGTTGATAAGGTCCTCCAGCCC-
upper sequence: AT5G55120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G02500.1 (Glycine max), 3'ss of exon 3
agtttcaggttcacattgttgatatttacttgagct--gaagaatcaattttctgtttcacattgttgatgtttggttgttggtgtgcattggtaataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
|| | || ||||| | | | | | || || || || | || || ||||||| | || ||||| ||| | | ||||| || || || | || |||||| |||| ||||| ||||| ||||| || ||||||||||||||||| |||||||| |||||||| || |||||||| |
---gtctgttttcttttgtttttgtcttcctatgcatagatatatggatggtatgatttctgagtttgatgtgt--tttgtggtg---att--ttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTCCGAGTTGACAAGGTCCTTCAACCCT
upper sequence: AT5G55120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G46230.1 (Glycine max), 3'ss of exon 3
agtttcaggttcacattgttgatatttacttgagc-tgaaga-atcaattttctgtttcacattgttgatg--tttggttgttggtgtgcattggtaataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
| || ||||| | | | | | || | | | || || || || | |||||| || || || || ||| | | ||||| || || || | || |||||| |||| ||||| || || ||||| || ||||||||||| ||||| |||||||| ||||| || || |||||||| |
--gtctgttttgtttttgtttttgtcttcctatgcatacatatatggatggcatgatttctgattttgatgtgttctgtggtgaatggtgatt--ttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCACCTCAAGAAGAGGCCAACTGAGTTCCGAGTTGATAAGGTCCTTCAACCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttctgtttcacattgttgatgtttggttgttggtgtgcattggtaataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
tgttgat putative branch site (score: 4)
taataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtttcaggttcacattgttgatatttacttgagctgaagaatcaattttctgtttcacattgttgatgtttggttgttggtgtgcattggtaataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - -gaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg