Sequence
atgc intronic sequence ATGC exonic sequencegtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19960.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 5
gtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------
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-----------tgttttttgaggtcatttttttaattgatgtcatttttaa-----ttataccatggtatatattg-attatatgaatgaaggatgtcttctttttaatatatatagTGGTGAGAGTGGAGCAGGAAAGACAGAAACTGCAAAGATTGCTATGCAGTATTTGGCTTCTCTTGGAGGTGGGGGTGGCATAGAATATGAGATCCTACAA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 5
gtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggt-gcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------
|||| | | | | ||| | |||| | || || || || ||| | | || | | | | | || | ||| || |||||||||||||| ||||| || || || ||||| |||||||| ||| ||||| | |||||||| ||||| || ||
------------------tgaggtcatttgggaaattgatggcattaatattctagtagcacccttactgattatgtgaagacgtgatgccgttttgattcttttgattttgatacagTGGTGAGAGTGGAGCAGGAAAAACAGAAACCGCAAAAATTGCTATGCAGTACCTGGCTTCCCTTGGAGGTGGAAGTGGCATTGAATACGAAATTCTTCAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
gtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtatt----ttgtggtgtatcct-tatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------
|||| | ||| | | ||| ||| ||| | ||||||||| ||| || ||| || | || | || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || ||
---------------------gacaagctctttcttggtgttccttaatcttgtg-tgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
gtaaagttgcattagttgtgagacactgag-actagtggatctgttgaataaag-tggtgcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------
|| | || | || | | ||| | || | ||| || | || ||||| | | | || | || || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || ||
-------------------gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 4
gtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgt---ggtgtatccttatcacaagATT--CTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------
|||| | ||| | || ||| ||| ||| | | || |||| ||| | | ||| | || | | || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || ||
---------------------gacaagctcttttttggtttcctttaatcttgtg-tgccccttaatcgtttattgtgtttgaattgggacctataataataattatcatgtacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 6
gtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------
| || | | | | || | | || | | || | | | | | | | | ||| | || |||| || || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||| | ||||| || ||||| || ||
-------ttcagcattaatatcaagctcaacttggt---tttcttaaccttgtgtgccccttaattgcatttgaattgggacacataattat-------tttcatctgcatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTACCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 5
-gtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------
|||| | | ||| | | ||||| || || ||| | |||| | | | | | | | || | ||| |||| ||||| ||| ||||||||| || || ||||||||||||||||||||||| || || ||||| |||||||| |||||||| ||||| ||||| ||||| ||
cttaaaatcg----ggttatatcaagttgagaaccctgaattggtt-agtaaaa--------ctattgtattgaatccttgataaatctaaatca----attct-tttgttcttccagTGGTGAAAGTGGAGCAGGGAAAACTGAGACGGCAAAGATAGCAATGCAATATTTGGCTGCCCTTGGTGGCGGTAGCGGAATAGAATATGAGATATTGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT
tccttatc CT-rich tract
tgtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG