Sequence
atgc intronic sequence ATGC exonic sequencegcaagtatcttaaataacttttatccatattgctatctctcatatttccaaagctctttgggaggttggatacttacgattctgatcatatttttcctttgtatctttattatcaatgtagGACGCGTTACTTTTCCACGCCAAGGAAAGGGCACAACCCACTTCAAGGAAGGGCATACTACCAACTTCTAGAGTGTCTTGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08660.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G05340.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------gcaagtatcttaaataacttttatccatattgctatctctcatattt-ccaaagctctttgggaggttg-gatacttacgattctgatcatat--ttttcctttgtatctttattatcaatgtagGACGCGTTACTTTTCCACGCCAAGGAAAGGGCACAACCCACTTCAAGGAAGGGCATACTACCAACTTCTAGAGTGTCTTGGT
|| || | | | | | | ||| | | ||||| | | | | ||||||| |||||| | | | | | | | | ||||||| |||| || || || | |||||| | ||||| || ||| ||||| || |||||||||||||||||||| |||||||||||||| ||||| ||||||||
gtgggtttctctattttaatattgattatttattatattcttggtgtttccttcattgatactccaatcttcatttttaaattatttgtttatttatttatttattttgtatatgaggttgtgatactaatgccttcaaacttttgatcttcctttttatcgtttttttct-tatagGACAAGATACTTCTCTCAGCCTAGGAAGGGACACAACCCACTTCAAGGAAGAGCATACTACCAACTCCTAGAATGTCTTGGG
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G27540.1 (Glycine max), 3'ss of exon 2
--------------------------------------gcaagtatcttaaataacttttatccatattgctatctctca--tatttccaaagctcttt-------gggaggttg-gatacttacgattctgatcatat--ttttcctttgtatctttattatcaatgtagGACGCGTTACTTTTCCACGCCAAGGAAAGGGCACAACCCACTTCAAGGAAGGGCATACTACCAACTTCTAGAGTGTCTTGGT
| | |||| | | | | |||| || || | | | ||| | | | ||| ||||||||| |||||| || | | ||| | | ||||||| |||| || || || | ||||| | ||||| || ||| ||||| || ||||| |||||||||||||| |||||||||||||| ||||| || |||||
gtgggtttctctgttttgatattgattatttattatattcttggttcttccttcattatactccaaatcttcatttttaaattatctgtttatttattttgtacatgggaggttgtgatactaccgccttcaaacattttatcttcctttttatcatttttttct-tacagGACAAGATACTTCTCTCAGCCTAGGAAGGGACACAATCCACTTCAAGGAAGAGCATACTACCAACTCCTAGAATGCCTTGGG
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0068g01150.t01 (Vitis vinifera), 3'ss of exon 9
gcaagtatcttaaataacttttatccatattgctatctctcatatttccaaagctctttgggaggttggatacttacgattctgatcatatttttcctttgtatctttattatcaatgtagGACGCGTTACTTTTCCACGCCAAGGAAAGGGCACAACCCACTTCAAGGAAGGGCATACTACCAACTTCTAGAGTGTCTTGGT
|||| || || || || || || | || | | ||||| | || | | |||| | || | | || | |||||| || ||||| || || ||||||||||| ||||| |||||||||||||||||||| ||||| || |||||||| |||||
-----------------tccttattgat-ttagaggctttc---ttctcatgcttgttaaactgatgggatattgtttatcttcctttcccttttgactagttttatgatatttctcatagGACCCGATACTTCTCTACACCAAGGAAAGGACACAATCCACTTCAAGGAAGGGCATATTACCAGCTCCTAGAGTGCCTTGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatacttacgattctgatcatatttttcctttgtatctttattatcaatgtagGACGCGTTACTTTTCCACGCCAAGGAAAGGGCACAACCCACTTCAAGGAAGGGCATACTACCAACTTCTAGAGTGTCTTGGT
tttgtatctttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtatcttaaataacttttatccatattgctatctctcatatttccaaagctctttgggaggttggatacttacgattctgatcatatttttcctttgtatctttattatcaatgtagGACGCGTTACTTTTCCACGCCAAGGAAAGGGCACAACCCACTTCAAGGAAGGGCATACTACCAACTTCTAGAGTGTCTTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA