Sequence
atgc intronic sequence ATGC exonic sequencegttgtgtgccttcaaaatcttattttttctttcttttctctgagctatatccatttcgcagtcccattgtattgtttatagtccttgtaattagctgtacagtaacagttacagcctgcaaactcagtctcatgttatagatgtgtaaaatttgcagGGTGGGCATTTCTCTGGCATATACAGGAAGGTTCAACTGAAGCCGTTGAAATGGGTTAACGTACCAAAAAGTGATGGTGAAGGCGAAGAGGAACGCCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 13
gttgtgtgccttcaaaatcttattttttctttcttttctctgagctatatccatttcgcagtcccattgtattgtttatagtccttgtaattagctgtacagtaacagttacagcctgcaaactcagtctcatgttatagatgtgtaaaatttgcagGGTGGGCATTTCTCTGGCATATACAGGAAGGTTCAACTGAAGCCGTTGAAATGGGTTAACGTACCAAAAAGTGATGGTGAAGGCGAAGAGGAACGCCCAG
||| | | | || | || || |||| || ||| | |||||| | || | ||| || | | | | || | | |||| || || |||||||||||||||||||||||||| |||||||| ||| | ||||| | || ||| | || || | ||||| |||||||||| | ||| ||||| || |
---------------------------------------ctgcataacagcagctttg--gtt---ttatatttttcataat---tgtaataaaaaagacttcagacgtttca-tgtactacttttgttttcttttatt------caatat---cagGGTGGGCATTTCTCTGGCATATATAGGAAGGTCCAATTAAAGCCACTAAAGTGGATCAAAGTGGCCAAAAGCAATGGTGAAGGTGCAGAAGAACGACCTG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 15
gttgtgtgccttcaaaatcttattttttctttcttttctctgagctatatccatttcgcagtcccattgtattgtttatagtccttgtaattagctgtacagtaacagttacagcctgcaaactcagtctcatgttatagatgtgtaaaatttgcagGGTGGGCATTTCTCTGGCATATACAGGAAGGTTCAACTGAAGCCGTTGAAATGGGTTAACGTACCAAAAAGTGATGGTGAAGGCGAAGAGGAACGCCCAG
| | ||| | ||| ||| ||||| | | ||||| | || || ||| || | || | | | | | | ||| | ||||| |||||||||||||||||||| || ||||||||| | ||||| | || ||| | || || | ||||| | |||||||| ||||| ||||| || |
-------------------------------------------------cctgaataacagcagctttgaatt-tttat--ttttcataatt--ttaatca--aaaagtcttgagttgtttcatgtacttctttgttttcttttattcaatat-cagGGCGGGCATTTCTCTGGCATATATAGAAAGGTTCAATTAAAGCCACTAAAGTGGATCAAAGTGGCCAAAAGCAACGGTGAAGGTGAAGAAGAACGACCTG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 15
gttgtgtgccttcaaaatcttattttttctttcttttctctgagctatatccatttcgcagtcccattgtattgtttatagtccttgtaattagctgtacagtaacagttacagcctgcaaactcagtctc-atgttatagatgtgtaaaatttgcagGGTGGGCATTTCTCTGGCATATACAGGAAGGTTCAACTGAAGCCGTTGAAATGGGTTAACGTACCAAAAAGTGATGGTGAAGGCGAAGAGGAACGCCCAG
|| | | | | | | || | | ||||| || | || || | || || ||| |||| ||| |||| | || ||||| || ||||||||||| || || ||||||||||||| ||||| | || |||||||| || ||||||||| |||||||||| ||||| ||||| || |
----------------------------------------------------atgtgaaaattcaaaag-atcctcctcattcctt-tactacatcgttaagctgc--cctggatttgttctctttttcttgatgtcataaatgtttgctatc--cagGGGGGACATTTCTCTGGTATTTATCGGAAGGTTCAACTAAAGCCACTAAAGTGGGTTAAAGTTCCAAAAAGTAATGGTGAAGGTGAAGAAGAACGGCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacagttacagcctgcaaactcagtctcatgttatagatgtgtaaaatttgcagGGTGGGCATTTCTCTGGCATATACAGGAAGGTTCAACTGAAGCCGTTGAAATGGGTTAACGTACCAAAAAGTGATGGTGAAGGCGAAGAGGAACGCCCAG
cagtaac putative branch site (score: 2)
tgtaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtgtgccttcaaaatcttattttttctttcttttctctgagctatatccatttcgcagtcccattgtattgtttatagtccttgtaattagctgtacagtaacagttacagcctgcaaactcagtctcatgttatagatgtgtaaaatttgcagGGTGGGCATTTCTCTGGCATATACAGGAAGGTTCAACTGAAGCCGTTGAAATGGGTTAACGTACCAAAAAGTGATGGTGAAGGCGAAGAGGAACGCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA