Sequence
atgc intronic sequence ATGC exonic sequencegtttgtggagactgcctgcatgtattacatatgtattattgtttctgttctaagaagacatttcttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38280.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
------------------------------------------------------------------------------------------gtttgtggagactg-cctgcatgtattacatatgt------attattgtttctgttctaagaagacatttcttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC
|| ||| || || ||| | || | | | | | ||| ||||| | | | | |||| |||||||||||||| ||||| ||| | ||||||||||| |||||||| |||||||||||||| || || || |||||||| | |||| || |||||||| |
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC
upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
--------------------------gtttgtggagactgcctgcatgtattacatatgtattattgtttctgttctaagaagacatttc---ttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC
| | | | | | |||| | | | |||| || || || | | || | ||| |||||||||||||| ||||| ||| ||||||||||||| || ||||| || || || || ||||| ||||| ||| ||| | ||||||| ||||| ||
aggcaacaccaccagcaaatggcataaccttttgcacttcagtttctttattttgaaaga--tgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT
upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 15
------------------gtttgtggagactgcctgcatgtattacatatgtattattgtttctgtt---ctaagaagacatttcttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC
| | | || | || || | | || | | || || |||| | || || ||| | || ||||||||||||||| ||||| || ||||||||||| || |||||| | || || || ||||| || |||||| |||||||| | | || ||||||||||| |
gtaaaaagggagatgatgctgttttgaatatatctacactgacttgat-tattccatagtatctgattggctgtgattgcatgttggtt-acagATTGGTCTGGCTATGTCTCCTCTGAGCAACAATTCCTTGTTTTTGGACTATCATCGGAATCCTTTTCCTATGTTTTTCCTTCGGGGCCTCAATGTTTCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgtattacatatgtattattgtttctgttctaagaagacatttcttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC
catttctttt CT-rich tract
attacatatgtattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtggagactgcctgcatgtattacatatgtattattgtttctgttctaagaagacatttcttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG