Sequence
atgc intronic sequence ATGC exonic sequencegtaatgatttcaaactatgtcaatatggaatctgaagctagaaaacctttcttttccggctctttgattggactaattcgtacttttttcttttcagTGACGGAACTGTGTGAGTATGCTGCAAACGTTGATATTGCAATTGCGAGAGAGTCAATTCGAGCAGTTGGAAAGATTGCTTTGCAACAGTATGATGTAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G11490.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G11490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G029077_T01 (Zea mays), 3'ss of exon 5
gtaatgatttcaaa--ctatgtcaatatggaatctgaagctagaaaacctttcttttccggctctttgattggactaattcgtac-ttttttcttttcagTGACGGAACTGTGTGAGTATGCTGCAAACGTTGATATTGCAATTGCGAGAGAGTCAATTCGAGCAGTTGGAAAGATTGCTTTGCAACAGTATGATGTAAA
||| | | | |||| || | | ||| ||| || || | ||| | | | || | | ||| || |||| || ||||| ||||| ||||||| ||| |||||| | ||||||| |||||||| || || ||||||||||| || || |||| ||||||||||| ||
gtatatgcctgatattctatttccaactataatttgatatgttttcttattaattactattatttttaaaatatcgattttgcatgtttctttccaccagTCACTGAACTATGTGAATATGCTGGAAATGTTGATGTACCAATTGCAAGAGAGTCTATCCGGGCAGTTGGAAAAATAGCACTGCAGCAGTATGATGTTAA
upper sequence: AT5G11490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------gtaatgatttcaaactatgtcaatatggaatctgaagcta-gaaaacctttcttttcc------ggctctttgattggactaattcgtactttt------ttcttttcagTGACGGAACTGTGTGAGTATGCTGCAAACGTTGATATTGCAATTGCGAGAGAGTCAATTCGAGCAGTTGGAAAGATTGCTTTGCAACAGTATGATGTAAA
| ||| || || | || | | || |||| | | ||| ||||| | || | | |||| || || | || | | || ||||||||||| | ||||| ||||||||||| ||||||||| | ||||| ||||||||||| || || ||||| || || || |||| ||||||||||| ||
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgca---tgagtaactgtgcgttctgtccttttggtgacccacctttttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacctttcttttccggctctttgattggactaattcgtacttttttcttttcagTGACGGAACTGTGTGAGTATGCTGCAAACGTTGATATTGCAATTGCGAGAGAGTCAATTCGAGCAGTTGGAAAGATTGCTTTGCAACAGTATGATGTAAA
gactaat putative branch site (score: 2)
ttcgtacttttttctt CT-rich tract
tacttttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgatttcaaactatgtcaatatggaatctgaagctagaaaacctttcttttccggctctttgattggactaattcgtacttttttcttttcagTGACGGAACTGTGTGAGTATGCTGCAAACGTTGATATTGCAATTGCGAGAGAGTCAATTCGAGCAGTTGGAAAGATTGCTTTGCAACAGTATGATGTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG