Sequence
atgc intronic sequence ATGC exonic sequencegtacactttatgtttcttgtctctttatttgcataggaccttgtttaagctcattgtaattggtgattctttatgaagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCAAAATATTGTCCTCTTGGAGCTCCTCCAAGGTCAACTATTGCTGCGGCTTTTAGTACTGATGGAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43930.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43930.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 2
------------------------------------------gtacactttatgtttcttg----tctctttatttgcataggaccttgttt--aagctcattgtaattggtgattctttatgaagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCAAAATATTGTCCTCTTGGAGCTCCTCCAAGGTCAACTATTGCTGCGGCTTTTAGTACTGATGGAAGA
| | | || ||| | | ||| || | | || ||| | | ||| || || ||| ||||||||||| |||||||||| |||||| ||||| || ||||||||| | | ||||||||||||| |||||||| || || ||||| | ||||| | |
gtacttacactaatttagtccataagttatattgaggaaaaagcatgcctttgagaatttgaaattttgttttcttcaagaagagtcaattttggggactaatgtctctgacaatgattttc--agGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGGTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
upper sequence: AT5G43930.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
--------------------------------------------gtacactttatgtttct----tgtctctttatttgcataggaccttgtttaagctcattgtaattggtgattctttatgaagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCAAAATATTGTCCTCTTGGAGCTCCTCCAAGGTCAACTATTGCTGCGGCTTTTAGTACTGATGGAAGA
| | ||| | | | | | |||| || | | |||| | | | | | | | |||| | |||||||||| |||||||||| |||||| ||||| || ||||||||| | ||||||||||||| |||||||| || || ||||| | ||||| | |
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatca-gGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
upper sequence: AT5G43930.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtacactt-tatgtttcttgtctct--ttatttgcataggaccttgtttaagctcattgtaattggtgattctttatgaagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCAAAATATTGTCCTCTTGGAGCTCCTCCAAGGTCAACTATTGCTGCGGCTTTTAGTACTGATGGAAGA
|| | | | |||| ||| ||| || || | | | ||| || || || | || | || | | ||||| |||||||| ||||||||||||||||| || | ||||||||||| ||||||| ||||| |||||||| || || || ||| | ||||||| |
tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttctttttatctttctttctttcttttttgttcct--tttctgttctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttgcataggaccttgtttaagctcattgtaattggtgattctttatgaagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCAAAATATTGTCCTCTTGGAGCTCCTCCAAGGTCAACTATTGCTGCGGCTTTTAGTACTGATGGAAGA
ttctttat CT-rich tract
attgtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacactttatgtttcttgtctctttatttgcataggaccttgtttaagctcattgtaattggtgattctttatgaagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCAAAATATTGTCCTCTTGGAGCTCCTCCAAGGTCAACTATTGCTGCGGCTTTTAGTACTGATGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA