Sequence
atgc intronic sequence ATGC exonic sequencegttagttacagaggacagagggcctttgcaatgtatttcaatagcttcgtgtgccatcataacacaattttttcggtttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62410.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 16
gttagttacagaggacagagggcctttgcaatgtatttcaatagcttcgtgtgccatcataacac--aattttttcggtttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
|| | | | ||| | || | | ||| | | | || | || || ||| | ||| | |||||||||| |||||||||| || |||||| || ||| | ||||||||||| ||||| ||| ||||||| || ||| ||||||| ||| |
---------gtgggtcttac--cttttctagtgataacctaggacttactttaaaagcagcatacgtaaaccttttgttttcatctgcagAATGACAAGTCAAAAATCAAGACAGTGATAGAAGAGTTGGATGAGAAGAAGAAAGAGACCTTGAAAGTCACATGGCTTAAAGTAAACAA
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G006452_T02 (Zea mays), 3'ss of exon 10
gttagttacagaggacagagggcctttgcaatgtatttcaa-tagcttcgtgtgccatcataacacaattttttcggtttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
| | | | | | || || | | || ||| || | ||| |||| || || | | |||||||||| ||||||||| ||||||||| |||||| | ||||||||||| || ||||| |||| || |||||| | ||||| ||| |
--gtatctcctatcatgtacagttttcttgataaactgaaagtagttt----taatatctgggcacatacctt---gtctcatctgcagAATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAA
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 17
gttagttacagaggacagagggcctttgcaatgtatttcaatagcttcgtgtgccatcataacacaattttttcggt---ttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
| ||| |||| |||||| | | ||| | || | || || | ||||||||||||||||||| || ||||||| ||| ||||| || ||||| ||||||||||| || || || || || ||||| ||| | ||||| || |
--------------------gtgattttcaatctatttccacattttctaactttcttgtataaatgcttaatctatttattttttcctagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 16
gttagttacagaggacagagggcctttgcaatgtatttcaatagcttcgtgtgccatcataacacaattttttcggtttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
| | | || |||| | || | | || | | || || || | | | ||| ||||||||||| |||||||||| || ||||| || ||||| ||||| ||||| || ||||| | || ||||||||| |||||||||| |
-------------gtttgtagctct---caatctgtt--gacatgttgtcatactatgattttacttatgataatatgcctttaatagAATGACAAGTCAAAAATCAAGATGGTGATTGAAGAGCTGGATGAAAAGAAGAAGGAAACATTAAAGGTTACTTGGACTAAAGTTAACAA
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: EFJ04936 (Selaginella moellendorffii), 3'ss of exon 16
gttagttacagaggacagagggcctttgcaatgtattt-caatagcttcgtgtgccatcataacacaattttttcggtttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
| || || | | | || | |||| | | || |||| | | | || |||| ||| | |||||| |||||| |||||||||||||||||||||||| || || |||||||||||| | || ||| |
---------------------------gtaagctaatcgtgaaatttttctttgccgt-gtgacgtg----catcggctgctggc--agGATGATAAAGCGAAAATCGAAGCGGTGATCAGGGAGCTTGATGAGAAGAAAAAAGAGACTCTAAAAGTTACTTGGCAACACGTGAACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttcaatagcttcgtgtgccatcataacacaattttttcggtttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
tcataac putative branch site (score: 2)
ttttttcggttttttt putative PPT
ataacacaatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttacagaggacagagggcctttgcaatgtatttcaatagcttcgtgtgccatcataacacaattttttcggtttttttcctagAATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA