Sequence
atgc intronic sequence ATGC exonic sequence...ataagcttttttcacttctatgctttgctcatctgtttgactacatccttgattagactcttctaaactgcatgacctaattcatctgtacttttcccagTGTTACTACTCTGATGCGGCTATAGCTGATGGGTACTTCAGTGTGTTGGCTGAGGTTTACATGCGACAAGAAATACCAAAATGTGAAATCCAGAGGCTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15680.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15680.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G344967_T01 (Zea mays), 3'ss of exon 16
----ataagcttttttcacttct--atgctttgctcatctgtttgactacatccttgattagactcttctaaactgcatgacctaattcatctgtacttttcccagTGTTACTACTCTGATGCGGCTATAGCTGATGGGTACTTCAGTGTGTTGGCTGAGGTTTACATGCGACAAGAAATACCAAAATGTGAAATCCAGAGGCTCT
|| | | || |||||||| ||| ||| ||| | | || || |||| || || |||| | ||| || || || || ||| | |||| |||| | || | ||||| ||||| || |||||||| ||||||| || |||||||| || || || |||||||||||||||||||| ||
gtaaatgatatgttgtcacttctcaatgacttgggcattattctatttatatgcttg-ctaccagctgttaaatcac-tgatct--tttgtcaataatttgc--agTGCTACTCTCCAGACCCTCAAATAGCAGATGGCTATTTCAGTGTTCTGGCTGAAGTCTACATGCGCCAGGAGATTCCAAAATGTGAAATCCAGAGACTTG
upper sequence: AT5G15680.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA19G04970.1 (Glycine max), 3'ss of exon 12
ataagcttttttcacttctatgctttgctcatctgtttgactacatccttgattagactcttctaaactgcatgacctaattcatctgt-acttttcccagTGTTACTACTCTGATGCGGCTATAGCTGATGGGTACTTCAGTGTGTTGGCTGAGGTTTACATGCGACAAGAAATACCAAAATGTGAAATCCAGAGGCTCT
| || | || | | ||| | || | | | | | || | || | || | || | | | ||| ||||| ||| ||||| || | || |||| ||||||||||||||||| |||||||||| |||||||| ||||| |||||||| |||||||| ||||| | |
ctgcttttcagataattttttccttgtattatttctcttgtggagttatctgttttgtcatgctggcat-tatagcttatacaacttattgatttctgcagTGCTACCACTCTAATTCTTCTGTAGCCGATGGGTACTTCAGTGTACTGGCTGAGGTCTACATGCGCCAAGAGATACCAAACTGTGAAATACAGAGATTAT
upper sequence: AT5G15680.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv14s0083g00750.t01 (Vitis vinifera), 3'ss of exon 16
-ataagcttttttcacttctatgctttgctcatctgtttgacta-catccttgattagactcttctaaactgcatgacctaattcatct-gtacttttcccagTGTTACTACTCTGATGCGGCTATAGCTGATGGGTACTTCAGTGTGTTGGCTGAGGTTTACATGCGACAAGAAATACCAAAATGTGAAATCCAGAGGCTCT
|||| || ||| | || || | | || | | || | || | | ||| || | | || | ||||| | || ||| ||||| ||||| |||||||| || ||||||||||| |||||||||||| ||||||| || || ||||| || ||||| |||||||||||||| ||||| |||
ctgctactttgtttgcttg-gtatcttattcctgtcattaattttcaacttttgtaatacttatc--atgttcagggagtaattagcttcatattttcttcagTGCTACTATTCTGATGCTGCGATAGCTGATGGCTACTTCAGTGTGCTGGCTGAAGTCTATATGCGCCAGGAAATTCCAAAATGTGAAATTCAGAGACTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttgattagactcttctaaactgcatgacctaattcatctgtacttttcccagTGTTACTACTCTGATGCGGCTATAGCTGATGGGTACTTCAGTGTGTTGGCTGAGGTTTACATGCGACAAGAAATACCAAAATGTGAAATCCAGAGGCTCT
tctgtacttttccc CT-rich tract
taattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataagcttttttcacttctatgctttgctcatctgtttgactacatccttgattagactcttctaaactgcatgacctaattcatctgtacttttcccagTGTTACTACTCTGATGCGGCTATAGCTGATGGGTACTTCAGTGTGTTGGCTGAGGTTTACATGCGACAAGAAATACCAAAATGTGAAATCCAGAGGCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - -tgtttga
- - - - - - - - - - - - - - - - - - - - ctacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctaat