Sequence
atgc intronic sequence ATGC exonic sequence...agaatgtggtttatgactagatcaatgcaactagctttataatcagtagtgaagcctgtggaatttatacatgacttttcttctatgaaacgattgacagGAATCACATATTCACTCTCTGATGAACGTTCTACGGTATTGTAATCTTGACGAATCTCTTCAAGGAGAAGAAAGTCTGGTCTGCCAAAGCGCGTTGGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.1 |
intron # | 28 |
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 28
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 25
agaatgtggtttatgactagatcaatgcaactagctttataatcagtagtgaagcc-----tgtggaatttatacatgacttttcttctatgaaacgattgacagGAATCACATATTCACTCTCTGATGAACGTTCTACGGTATTGTAATCTTGACGAATCTCTTCAAGGAGAAGAAAGTCTGGTCTGCCAAAGCGCGTTGGATC
|| | | || ||| || || |||| | | | | | || || ||| || ||| | | |||||||||||| |||||||| ||||| ||||| ||||| || ||||||||| | || ||||| ||||||| |||||| ||||| || |||| | || | ||
--gataca-ctcaaga--agactgattcataagactttgtggcttagaattgctctgtaaatttgatcttcttactctgtttcacttgccttattttgttgacagGAATCGCATATTCATTCTCTCATGAATGTTCTTCGTTATTGTAATATGGAAGAATCCCTTCAAGAAGAAGAGAGTCTTGTTTGCCGTAATGCTCTAGAGA
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 41
agaatgtggtttat--gactagatcaatgcaactagc--tttataatcagtagtgaagcctgtggaatttatacatgacttttcttctatgaaacgattgacagGAATCACATATTCACTCTCTGATGAACGTTCTACGGTATTGTAATCTTGACGAATCTCTTCAAGGAGAAGAAAGTCTGGTCTGCCAAAGCGCGTTGGATC---
|| | | |||| ||| | | | ||| ||| | || ||| ||| ||| || ||| | |||||||||||| |||||||| ||||| ||||| ||||| || ||||||||| | || ||||| ||||||| |||| ||||| || |||| | || | ||
--gatacactcaagcagactgattcacaagattttgtggcttagaattgctctgtaaatttgtt--attcttactctgtttcacttgccgtattttgttgacagGAATCTCATATTCATTCTCTCATGAATGTTCTTCGTTATTGTAATTTGGAAGAATCCCTTCAAG---AAGAGAGTCTTGTTTGCCGTAATGCTCTAGAGAGAC
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 25
agaatgtggtttatgactagatcaatgcaactagctttataatcagtagtgaagcctgtggaattt--atacatgacttttcttctatgaaacgattgacagGAATCACATATTCACTCTCTGATGAACGTTCTACGGTATTGTAATCTTGACGAATCTCTTCAAGGAGAAGAAAGTCTGGTCTGCCAAAGCGCGTTGGATC
|| | | | | ||| | | | | || | | | || |||| |||| | |||| |||| | | ||||||||||||||||| ||||| ||||| ||||| || ||||||||| | || ||||||||| || ||||| || || || || | | || | || |
--gattcatccaaagtcaggttcataattttttgacatttgtatagaatttatcttagttttatttccatacttttgttttaacctattatttatattgcagGAATCACATATTCATTCTCTCATGAATGTTCTTCGTTATTGTAATTTGGATGAATCTCTTTTAGATGAAGAGAGCCTAGTTTGTTATAATGCTCTAGAGC
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 27
agaatgtggtttatgactagatcaatgcaactagctttataatcagtagtgaagcctgtggaatt-----tatacatgacttttcttctatgaaacg-attgacagGAATCACATATTCACTCTCTGATGAACGTTCTACGGTATTGTAATCTTGACGAATCTCTTCAAGGAGAAGAAAGTCTGGTCTGCCAAAGCGCGTTGGATC
| || || || ||| || ||| || || | ||||| | | | | || |||| | |||| |||| | |||||||||||||||||| || ||||| ||||| ||||| || ||||||||| || |||||||||| || ||||| || || || ||| | | || | || |
----tttgtaacataacaagaataaaacaa--agtcttgtggcaagtagcttggtttttagttttatttccatacttttgttttaacctattatgtatgttgacagGAATCACATATCCATTCTCTCATGAATGTTCTTCGTTATTGTAATTGGGATGAATCTCTTCTAGATGAAGAGAGCCTCGTTTGCTATAATGCTCTAGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagtgaagcctgtggaatttatacatgacttttcttctatgaaacgattgacagGAATCACATATTCACTCTCTGATGAACGTTCTACGGTATTGTAATCTTGACGAATCTCTTCAAGGAGAAGAAAGTCTGGTCTGCCAAAGCGCGTTGGATC
aatttatacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaatgtggtttatgactagatcaatgcaactagctttataatcagtagtgaagcctgtggaatttatacatgacttttcttctatgaaacgattgacagGAATCACATATTCACTCTCTGATGAACGTTCTACGGTATTGTAATCTTGACGAATCTCTTCAAGGAGAAGAAAGTCTGGTCTGCCAAAGCGCGTTGGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -ggtttat
- - - - - - - - - - - caatgca