Sequence
atgc intronic sequence ATGC exonic sequencegtaaggtttcatgaatttgtttagtcagctctccttttttcgtataccattactagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G74320.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g08760.1 (Oryza sativa), 3'ss of exon 3
gtaaggtttcatgaatttgtttagtcagctctccttttttcgtataccattactagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
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----gatgttggtaattcttggaatgggagcaattgcttaggtcatattctgtta--atattttgctgtaaataactgctgtcttgggatctcttttatccttcagGACTACGAGTATGCGAGTTTTAATCCTGTGGCATTTGACATTGCTAATCACTTCTGTGAGATGTCTGCTGATTATCATTCAGCCACACCTCATGTGCTGG
upper sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G087146_T01 (Zea mays), 3'ss of exon 3
gtaaggtttcatgaatttgtttagtcagctctccttttttcgtataccattac-tagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
| || | | || | || ||| || | | || | | | | || | | ||| | | || | || || | || | |||| ||||||||| | | | ||| || || || | |||||||| ||||||||||||||||||||||| |||||||| || |||||| || | |||
--acaacttgacagacctgcgagg--agttcttgttctaccaaatcttagaccatgttattcctgtaacttaatgccgccttgttgatcttttattctctg---cagGACTATGAATATGCGAGTTTTAACCCAGTCGCATTCGACATTGCTAATCACTTCTGTGAGATGGCTGCTGATTACCATACATCAACACCACATGTGTTGG
upper sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G46600.1 (Glycine max), 3'ss of exon 3
gtaaggtttcatgaatttgtttagtcagctctccttttttcgtataccattactagaaaaaatggatcctaact--ctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
| | ||| || | | | | | || | ||| | | |||||| | || | | || | ||| | | | || |||| ||||||||| | | |||||||||||||| | ||| || || || |||||||||||||||||||| | || ||||| ||| ||||| ||| | |
-----gctaaatgtatgaga--aactggtttactcttggttatattttgccaa-ggggtcaatggaccatagccagcaaatatgatttaatgctaccttttgcaacagGACTATGAATATGCTAGTTATAATCCTGTGGCATTTGATATAGCAAACCACTTCTGTGAGATGGCTGCTAACTATCACACAGAAGAGCCTCATATCCTTG
upper sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0084g00150.t01 (Vitis vinifera), 3'ss of exon 4
gtaaggtttcatgaatttgtttagtcagctctccttttttcgtataccattactagaaaaaatggatcctaactctgattt-tattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
| | | ||| | | || || | || ||| | ||| | || | ||| || | ||| | | ||| || | | | |||||||||| ||| || | || |||||||| |||||||||| || ||||||||||||||||||||||| || || || || ||||| |||||||| |||
tgactatcacttgatatgaatcaggcacttgtctgccttttagtcaatatttttggagcttaa-----ctagctgttattcatctaattctgctctctttac--cagGATTATGAGTATGCAAGTTACAATCCTGTCACTTATGACATAGCAAATCACTTCTGTGAGATGGCTGCTGACTATCATACAGAAACGCCTCACATTTTGG
upper sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S50_118V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaggtttcatgaatttgtttagtcagctctccttttttc---gtataccattactagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
|| | | ||||| | || | | | | | | || |||||| | | ||||||| || | || || |||||| ||| | ||||||| || || | | || || || || || | ||||||||| || || |||||||||||| |||||||||||||| |||| || || | |
--cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatcc-----ctaagcttctt-ttttgttgtattggag-cagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA
upper sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ23622 (Selaginella moellendorffii), 3'ss of exon 3
gtaaggtttcatgaatttgtttagtcagctctccttttttcgtataccattactagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
|| ||| ||| || || || || || | | | | | || | | | | ||| | | || |||| || || || | |||| ||||| ||||| | ||||||||| ||||||||||| ||||||||||||||||| ||||| ||| | || ||| |||
----------gtgcgtttcttt--caaggcctttttgcttggtggatcttctttc-------tcttctttagttttctcaatctaattaacgttggtgcttaacagGACTACGAGTACGCCAGCTACAATCCCGTGGCGTTTGACATTGCGAATCACTTCTGCGAGATGGCTGCCGATTATCACACGGAATCTCCCCACCGGCTGG
upper sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ05852 (Selaginella moellendorffii), 3'ss of exon 3
gtaaggtttcatgaatttgtttagtcagctctccttttttcgtataccattactagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
|| ||| ||| || || || || || | | | | | | || | | | | ||| | | || |||| || || || | |||| ||||| ||||| | ||||||||| ||||||||||| ||||||||||||||||| ||||| ||| | || ||| | |||
----------gtgcgtttcttt--caaggcctttttgcttggtggatcttctttc-------tcttccttagttttctcaatctaattaacgttggtgcttaacagGACTACGAGTACGCCAGCTACAATCCCGTGGCGTTTGACATTGCGAATCACTTCTGCGAGATGGCTGCCGATTATCACACGGAATCTCCCCACCGCCTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
taactctgattttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggtttcatgaatttgtttagtcagctctccttttttcgtataccattactagaaaaaatggatcctaactctgattttattattttgtcttataaaaaatagGATTATGAATATTCATGCTATAATCCTGTGGCTTATGACATTGCCAATCACTTCTGTGAGATGGCTGCCGATTACCACACTGAAACACCTCACATCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG