Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaagggacactcttttcgttgctaaagatacaagtcataatgtttcattttcaaccagtttgggttttttgtgttcttacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60690.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 5
---------gtaagaaagggacactcttttcgttgctaaagatacaagtcataatgtttcattttcaaccagtttgggtttttt---gtgttct-tacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
||| || | | | |||| | ||| | | || || || | | | || || |||| || | ||||| | |||||| | ||||| || ||||||||||||||||| ||| | || |||||||| ||||| ||||| || ||||| ||||||||||| ||||| |
tcttcatacgtatttggttgatgtgaatattttctagaaagctgaaagactttattgttttcagaaaattgttgggagattcttatagtgtgctatgcagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G469551_T02 (Zea mays), 3'ss of exon 6
--------------gtaagaaa---gggacactcttttcgttgct-aaagatacaagtcataatgtttcattttcaaccagtttgggttttttgtgttcttacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
|| ||| | ||| | | | || | | ||||| ||| | || | | || | || | || | | | |||| | || ||| | |||||||| ||||||||||| ||||| ||| |||| |||||||| | || ||||| || ||||| |||||||| || || || |
ttttttgccacatggttcaaaacttagaacattttctgaattttttggacatacagtctgtaaa---ttatctggaggtttcttacgattgct-tgct-tgatagATAGTGGAAATCTTGAAAGATCGTCCATCTTGGTTTCGTGATTGTCGGAGTCTTGAAGTCTATACAATGTTACCAGCTGGAAATGGTGGAACCATTGAAC
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 5
----------------gtaagaaagggacactcttttcgttgctaaagatacaagtcataatgtttcattttcaaccagtttgggttttt-------tgtgttcttacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
||| | ||| | ||||| || || || | ||| | | | | | | | |||| ||| | || || |||||||||||||||||| |||||||| ||||||||||||||||||||| ||||||| |||||||| |||||||| || ||||| ||||| || || || || |
gtaaattgacttagaagtatggtttggatttttttttcatttcttggtatgccagtgaatgtctgtaagctgtttggaatttgaatttctgaatgcctgattttcaacagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
-------------------gtaagaaagggacactcttt-tcgttgctaaagatacaagtcataatgtttcattttcaaccagtttgggttttt-------tgtgttcttacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
||| | ||| | ||| || | || || | ||| | | | || | | |||| ||| | || || ||||||||||||||||| |||||||| ||||||||||||||||||||| ||||||| |||||||| |||||||| || ||||| ||||| || || || || |
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------gtaagaaag---ggacactcttttcgttgctaaag-atacaagtcataatgtttcattttcaaccagtttgggt------------------tttttgtgttc---ttacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
|| |||| | ||| | || | | | | | || | || | |||||| || | | | | | ||||||| | | | ||||||||||||||||||||||||||| |||||||||||||| |||||| ||||||||||||||||||| ||||| || ||||| ||||| || || | || |
gtaagcttcagccaattatgtggtcaggtcatttatgaaaatttgaacatttttcttgatattttattgtaggacctttattttttcatgttataataatattagcatgctttgaaaagtaatatttttgtttgcgactgacagATTGCAGAGATCCTCAAAGATCGTCCATCTTGGTTCCGGGACTGTCGGAGCCTTGAAGTTTTCACCATGTTTCCAGCTGGAAATGGAGGAACTGTTGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacaagtcataatgtttcattttcaaccagtttgggttttttgtgttcttacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
ttttttgtgttctt CT-rich tract
ataatgtttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaagggacactcttttcgttgctaaagatacaagtcataatgtttcattttcaaccagtttgggttttttgtgttcttacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG