Sequence
atgc intronic sequence ATGC exonic sequence...gtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19960.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 5
gtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagattctatttctt----cttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
|||| | | | |||| | | | || | || |||| | || | ||| || | ||| || || | || || |||||||||||||| || || || ||||| || || |||||||| || |||||| |||||||||| || | || || ||||||||||| || |
--tgttttttgaggtcatttttttaattgatgtcatttttaattataccatg-gtatatattgat-tatatgaatgaaggatgtcttctttttaatatatatagTGGTGAGAGTGGAGCAGGAAAGACAGAAACTGCAAAGATTGCTATGCAGTATTTGGCTTCTCTTGGAGGTGGGGGTGGCATAGAATATGAGATCCTACAA
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 5
gtgagacactgagactagtggatctgttgaataaagtggt-gcttccagtttgtgtattttgtggtgtatccttatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
|||| | | | | ||| | |||| | || || || || ||| | | || | | | | | || | ||| || |||||||||||||| ||||| || || || ||||| |||||||| ||| ||||| | |||||||| ||||| || || ||||| || || ||| ||
-tgaggtcatttgggaaattgatggcattaatattctagtagcacccttactgattatgtgaagacgtgatgccgttttgattcttttgattttgatacagTGGTGAGAGTGGAGCAGGAAAAACAGAAACCGCAAAAATTGCTATGCAGTACCTGGCTTCCCTTGGAGGTGGAAGTGGCATTGAATACGAAATTCTTCAG
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
gtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtatt----ttgtggtgtatcct-tatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
|||| | ||| | | ||| ||| ||| | ||||||||| ||| || ||| || | || | || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || || || |||||||| | |||
----gacaagctctttcttggtgttccttaatcttgtg-tgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 4
gtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgt---ggtgtatccttatcacaagatt--ctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
|||| | ||| | || ||| ||| ||| | | || |||| ||| | | ||| | || | | || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || || || |||||||| | |||
----gacaagctcttttttggtttcctttaatcttgtg-tgccccttaatcgtttattgtgtttgaattgggacctataataataattatcatgtacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
gtgagacactgag-actagtggatctgttgaataaag-tggtgcttccagtttgtgtattttgtggtgtatccttatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
|| | || | || | | ||| | || | ||| || | || ||||| | | | || | || || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || || || |||||||| | |||
--gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 6
gtgagacactgagactag--tggatctg--ttgaataaagtggtgcttccagtttgtgtattttg-tggtgtatccttatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
| || | | | | | | || || ||| | ||| || | || |||| | | | | | || | || || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||| | ||||| || ||||| || || || |||||||| | |||
-ttcagcattaatatcaagctcaacttggttttcttaaccttgtgtgccccttaattgcatttgaattgggacacataattat----tttcatctgcatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTACCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
upper sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 5
-------gtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
| | | | | | | | | ||||| | || | | | | | | | || | ||| |||| ||||| ||| ||||||||| || || ||||||||||||||||||||||| || || ||||| |||||||| |||||||| ||||| ||||| ||||| || |||||||||||| | ||
cttaaaatcgggttatatcaagttgagaaccc--tgaattggttagtaaaactattgtattgaatccttgataaatctaaatca----attct-tttgttcttccagTGGTGAAAGTGGAGCAGGGAAAACTGAGACGGCAAAGATAGCAATGCAATATTTGGCTGCCCTTGGTGGCGGTAGCGGAATAGAATATGAGATATTGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtttgtgtattttgtggtgtatccttatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
ttctatttcttcttcc CT-rich tract
attctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - gaataaa
- - - - - - - - - - - - - - - - - - - - - - - agtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaagat