Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcagctagtcctactatcaatttgtgagatattctttcttccaccatgtgtttatgagcgttttatggtttgtcttcagACCACCTGGCTTGAGTGCATTCAAGAACCCGGTGAAATTATCTTTGTTCCCAGTGGATGGCATCATCAAGTATATAACTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G19010.1 (Glycine max), 3'ss of exon 9
gtaaatcagctagtcctactatcaatttgtgagatattctttcttccaccatgtgtttatgagcgttttatggtttgtcttcagACCACCTGGCTTGAGTGCATTCAAGAACCCGGTGAAATTATCTTTGTTCCCAGTGGATGGCATCATCAAGTATATAACTTG
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-----------------------------------------------------------------gtttgta-tgtgtgtgctggctatctggttagAATGCACAGAAGATGCAGGTGAAATTATATTTGTTCCCAGTGGATGGTATCATCAATTTCATAATTTG
upper sequence: AT5G63080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G35940.1 (Glycine max), 3'ss of exon 7
gtaaatcagctagtcctact-----atcaat------ttgtgagatattctttcttccaccatgtgtttatgagcgttttatggtttgtcttcagACCACCTGGCTTGAGTGCATTCAAGAACCCGGTGAAATTATCTTTGTTCCCAGTGGATGGCATCATCAAGTATATAACTTG
|||||| | | | | |||||| || | | || |||| ||| | || | | |||| | || || | ||| | | |||| | || |||| ||| | | ||||||||||| |||||||| ||||||||| |||||||||| |||| |||
gtaaatttctagtttccattttctcatcaatcttattttttcaattagacttttttctgcttcagccttcagtgggtttgtttgt--gtatgcagGCTATCTGGTTAGAATGCACACAAAATGCAGGTGAAATTATATTTGTTCCAAGTGGATGGTATCATCAAGTTCATAATTTG
upper sequence: AT5G63080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g08880.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------------------gtaaatcagctagtcctactatcaatttgtgag-atattctttctt-ccaccatgtgtttatgagcgtttt-atggtttgtcttcagACCACCTGGCTTGAGTGCATTCAAGAACCCGGTGAAATTATCTTTGTTCCCAGTGGATGGCATCATCAAGTATATAACTTG
|| ||| | | | |||| | ||||| | | | ||||| | | | || | ||| | | ||| | ||| | || ||||||||||||| | ||||||||||||||| |||||||||||| |||||||||| | || ||
gtaatgcaccagtctgaactcatgtcctttgttcatcttgtgtgtttataatttttttattctcaatctcattaaccagtctaggtcaagtgatttcctcagttatttttacttatatttctacatgttttcatgtacatgtttgtgtctccatgtgacatttgcagGCTGTTTGGTTAGAATGCATTCAAGAACAAGATGAAATTATCTTTGTGCCCAGTGGATGGTATCATCAAGTTCACAATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagatattctttcttccaccatgtgtttatgagcgttttatggtttgtcttcagACCACCTGGCTTGAGTGCATTCAAGAACCCGGTGAAATTATCTTTGTTCCCAGTGGATGGCATCATCAAGTATATAACTTG
tttgtcttc CT-rich tract
tattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcagctagtcctactatcaatttgtgagatattctttcttccaccatgtgtttatgagcgttttatggtttgtcttcagACCACCTGGCTTGAGTGCATTCAAGAACCCGGTGAAATTATCTTTGTTCCCAGTGGATGGCATCATCAAGTATATAACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA