Sequence
atgc intronic sequence ATGC exonic sequencegtaccccacccaactttaggtgctataagtattcgattttcctagtaccaagtggccttccactgctcatcttattttctgttttggttgaacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G44240.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 19
gtaccccacccaactttaggtgctataagtattcgattttcctagtaccaagtggccttccactgctcatcttattttctgttttggttgaacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCA
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------tatccatcagtaatctacctgggccctagttttagtaaacattgtgtaattgatggatttctatttc--ccagtgcttatgttg---tcgtaattc-attttgtagCTTGTAAAGCTTCTAAAATCATGTGACTATCGAACTTTGGCTATTGGAGATGGTGGGAATGATGTCAGGATGATACAACAGGCTGATATTGGTGTAGGAA
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os04g28460.1 (Oryza sativa), 3'ss of exon 15
gtaccccacccaactttaggtgctataagtattcgattttcctagtaccaagtggccttccactgctcatcttattttctgttttggttg--aacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCA
| | || || | | ||| | | | | | | | ||||| | | || | ||| | | | | | ||| | |||| || | ||||| || ||| | ||| || ||||||||||| ||||| ||||||||||||||||| || | || | ||||| || || |
-------------ttacaattgtaccaaatcatgaattcacaactcatgcttttgatatataggagt-atcttttagtgaattaaaataaataacatccttcgcatttgtgcagCTTGTTGGGCTCCTGAAATCTGTCGGTTACCTAACTCTAGCAATTGGTGATGGTGGTAATGATGTAAGAATGATTCAAGAGGCAAACATTGGAGTTGGGA
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G479163_T01 (Zea mays), 3'ss of exon 1
gtaccccacccaactttaggtgctataagtattcgattttcctagtaccaagtggccttccactgctc-atcttattttctgttttggttgaacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCA
| | | || | || | | || | | ||| || | | ||| | | || | ||| || | | | | || |||| | | | || || || || |||||||| | ||||| ||||| ||||||||||||||||| |||||||| || ||||| ||||| || || |
-----------tattgaaagttgacttagagtaaagctaaaataagataatttggaatt--attactctgtttctccttggaaggtacttgccctaacatcctgtttccatagCTAGTGAAGCTTCTGAAGTCATGTGACTATCGAACTTTGGCAATCGGTGATGGTGGGAATGATGTAAGGATGATACAACAGGCTGACATTGGTGTAGGAA
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 19
gtaccccacccaactttag-gtgctataagtattcgattttcctagtaccaagtggccttccactgctcatcttattttctgttttggttgaacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCA
||| | | ||| | || | || | | || | | | | | | ||| || || | || ||| | || ||| | || | ||||||||||| || |||||| |||| | || |||||||| ||||||||||||||||| ||||||||||||||||||||||| || ||||
-----ttctgtaacgggaacataatattgctgtttgtattattctgctctaatttatcagaaaataatagcactgattt--gtcctg--tatacctttactta----ttgcagCTTGTACAGATCTTAAAATCATGTGATTATAGAACATTGGCTATTGGTGATGGTGGGAATGATGTAAGGATGATACAGCAAGCTGATATTGGTGTGGGCA
upper sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 19
gtaccccacccaactttag-gtgctataagtattcg-attttcctagtaccaagtggccttccactgctcatcttattttctgttttggttgaacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCA
|| |||| | | || | || | ||| | | || | | | | | | ||| || ||| | || ||| || | || ||| | || | ||||||||||| || |||||| |||| | || |||||||| ||||||||||||||||| |||||||| |||||||||||||| || ||||
------tccctaactggaacatattactgctgtttgtattatttcttctctaatttatcagaaaataatagcactgattt--gtcttg--tataccttta-cttg---ttgcagCTTGTACAGATCTTAAAATCATGTGATTATAGAACATTGGCTATTGGTGATGGTGGGAATGATGTAAGGATGATACAACAAGCTGATATTGGTGTGGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccactgctcatcttattttctgttttggttgaacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCA
ttattttctgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccccacccaactttaggtgctataagtattcgattttcctagtaccaagtggccttccactgctcatcttattttctgttttggttgaacttttggctcgactttacagTTAGTTGAAATCTTAAAATCCTGCGATTATCGAACCCTTGCAATTGGTGACGGTGGGAATGATGTAAGAATGATACAGCAAGCTGATATTGGGGTCGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT