Sequence
atgc intronic sequence ATGC exonic sequencegtgagttctttctcttacggtttcatattatcgctttttcgactcggttatgcggtgtgtgtgtgatcagtcgttgttttgtttcttcagATTCCAGAAGATCTTCATTTTGTGCTAAGGATGAGGCAAATGTTTGAATCAATTGGTTACAGATCAGGTTTTTACCTCTCACAGCTCTTCTCTTCAAACC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53900.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------------------------------------------------gtgagttctttctcttacggtttcatattatcgcttt-ttcgactcggttatgcggtgtgtgtgtgatcagtcgttgttttgtttcttcagATTCCAGAAGATCTTCATTTTGTGCTAAGGATGAGGCAAATGTTTGAATCAATTGGTTACAGATCAGGTTTTTACCTCTCACAGCTCTTCTCTTCAAACC
| | || | || ||||| || | | | | | | ||| |||| | | ||||| | ||| ||||||||| |||||||| | ||||||||| || ||||| || | |||||||| |||| ||| ||| ||||| |||||||| || |||||||||||||
gtgagttaattaattagtaccactttttctctccctccccaaaagccatttttactcattttaagtttacttatttgatatgttaattttaaaagttacattcactagttttaaacagttgttatagctattcattggatggaagaatctgccacaaaaaaatatcaaatgtttgat-attttttgttctattt--tcagATTCCTGAAGATCTCCGTTTTGTGCTTAGAATGAGACACACTTTTGAATCCCTTGGCTACCAATCTGGTTTCTACCTCTCTCAACTCTTCTCTTCAACAA
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 6
------------gtgagttctttctcttacggtttcatattatcgctttttcgactcggttatgcggtgtgtgtgtgatcagtcgttgttttgtttcttcagATTCCAGAAGATCTTCATTTTGTGCTAAGGATGAGGCAAATGTTTGAATCAATTGGTTACAGATCAGGTTTTTACCTCTCACAGCTCTTCTCTTCAAACC
|| | | | |||| | | | || | ||| || | || ||| |||| | || | | | | ||||||||||||||| || |||||||||||||| ||||| || | |||||||| | || || |||||| || |||||||| || |||||||||||||
gttaaagaatatgttgttaatatttctttcattagtagatgaatctctttcacaccaacaaaagcatcaaatgtttgat--attttttctctctgttctcagATTCCAGAAGACCTCCATTTTGTGCTAAGAATGAGACACACTTTTGAATCTCTAGGCTATCAATCAGGGTTCTACCTCTCCCAACTCTTCTCTTCAACAA
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------gtgagttctttctcttacggtttcatattatcgctt--tttcgactcggttatgcggtgtg-tgtgtgatcagtcgttgtt--ttgtttcttcagATTCCAGAAGATCTTCATTTTGTGCTAAGGATGAGGCAAATGTTTGAATCAATTGGTTACAGATCAGGTTTTTACCTCTCACAGCTCTTCTCTTCAAACC
||||| || || || | | | | | | | || | | | | | || | | || || || | | |||||||||| ||||| || ||||||||||| || ||| | || | |||||||| |||| ||| ||| ||||| |||||||| || |||||||||||||
gtgagttaattaatatgtatcactttttctcctccaaaaaatcatttttactcattttaagtttacttatttgacatggtaattttaagagttacatccgctagttttgtacagtttttatagatattgattggatattagaatctgacacaaagtttgatatttttggttctattttcagATTCCTGAAGACCTCCATTTTGTGCTTAGAATGCGACACACTTTTGAATCCCTTGGCTACCAATCTGGTTTCTACCTCTCTCAACTCTTCTCTTCAACAA
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------------------gtgagttctttctcttacggttt-catattatcgctttttcgactcggttatgcggtgtgtgtgtgatca-gtcgttgttttgtttcttcagATTCCAGAAGATCTTCATTTTGTGCTAAGGATGAGGCAAATGTTTGAATCAATTGGTTACAGATCAGGTTTTTACCTCTCACAGCTCTTCTCTTCAAACC
||| | |||| | ||| |||| || ||| | || ||| | | ||||| | | || ||| | |||||| || ||||| |||||||||||||| || ||| |||| | |||||||| |||| || ||| || || |||||||| ||||||||||||||||
gtgagtttcatttgtttttgtgctttgatcatctcttgtcctgctagtaattcttgatatttttcagattttgttgatatatgtatgcgtttgagcctttgtttccttgaaaggagttgatctcattgagattatgtatgctcagATACCGGAAGACCTTCATTTTGTGCTGAGAATGCGGCATACCTTTGAATCTCTTGGGTATCAATCTGGGTTCTACCTCTCCCAGCTCTTCTCTTCAACTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcgactcggttatgcggtgtgtgtgtgatcagtcgttgttttgtttcttcagATTCCAGAAGATCTTCATTTTGTGCTAAGGATGAGGCAAATGTTTGAATCAATTGGTTACAGATCAGGTTTTTACCTCTCACAGCTCTTCTCTTCAAACC
ttgttttgtttcttc CT-rich tract
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttctttctcttacggtttcatattatcgctttttcgactcggttatgcggtgtgtgtgtgatcagtcgttgttttgtttcttcagATTCCAGAAGATCTTCATTTTGTGCTAAGGATGAGGCAAATGTTTGAATCAATTGGTTACAGATCAGGTTTTTACCTCTCACAGCTCTTCTCTTCAAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC