Sequence
atgc intronic sequence ATGC exonic sequencegtaatggttttaaccatatgaggatgataaagttccacaattttcttctgttcaatgatcacaattgaaacatttcaaatcgtttggcagATGTCCCTGAAGGTTGTACCATCATAAGAGAACACATACCGATCACAAACCTTTTCACATGTGTATGGTTCAACGAGGTAGATCGGTTTACTTCAAGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G53040.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G53040.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 7
-gtaatggttttaaccatatgaggatgataaagttccacaattttcttctgttcaatgatcacaattgaaacatttcaaatcgtttggcagATGTCCCTGAAGGTTGTACCATCATAAGAGAACACATACCGATCACAAACCTTTTCACATGTGTATGGTTCAACGAGGTAGATCGGTTTACTTCAAGAGA
| || | | ||| || ||| || ||| || || ||| ||| || || ||| | | |||| ||||||||||||||||||| |||||| ||||| ||||| || ||||| || || |||||||| | |||||||| || || || || || || || || ||
gtcagtgatct----cattgaagtatggcgaaa----acagttcagttactttctgagattttaactgtcctttttgcattggttt---agATGTCCCTGAAGGTTGTGTCATCATCAGAGAGCACATTCCCATCACGAATCTCTTCACATGCCTTTGGTTCAATGAAGTTGACCGTTTCACCTCCAGGGA
upper sequence: AT1G53040.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G044866_T01 (Zea mays), 3'ss of exon 7
gtaatggttttaaccatatgaggatgataaagttccacaattttcttctgttcaatgatcacaattgaaacatttcaaatcgtttggcagATGTCCCTGAAGGTTGTACCATCATAAGAGAACACATACCGATCACAAACCTTTTCACATGTGTATGGTTCAACGAGGTAGATCGGTTTACTTCAAGAGA
|| | | | | | || || | | | | ||| | | |||| || ||||| | || ||||||||||| ||||| ||| ||||| ||||| ||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| || || || || ||
gtcagtgatctcatcagattacggtaa--aagcgcttcggttttttt----------------gctgaaatccctttgctccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACCTGTTCACGTGCGTATGGTTCAATGAGGTTGATCGCTTCACCTCCAGGGA
upper sequence: AT1G53040.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 7
gtaatggttttaaccatatgaggatgataaagtt-ccacaattttcttctgttca--atgatcacaattgaaacatttcaaatcgtttggcagATGTCCCTGAAGGTTGTACCATCATAAGAGAACACATACCGATCACAAACCTTTTCACATGTGTATGGTTCAACGAGGTAGATCGGTTTACTTCAAGAGA
|| | | | | || || | | | |||| || | || ||| | ||| | | || | | | ||| | | || |||||||||||||||| ||| ||||| ||||||||||| || ||||| ||||| ||||| || |||||||||| || || ||||| || || || || ||
gtcagtgaactcatcagattatggtaataacgtcgcttcagtttcttgctggaaatcctaatgctgagcggccccttttgcttggcatg-cagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACCTCTTCACGTGCTTATGGTTCAATGAAGTTGATCGCTTCACCTCCAGGGA
upper sequence: AT1G53040.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G35300.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------gtaatggttttaaccatatgaggatgataaagttccacaattttcttctgttcaatgatcacaattgaaacatttcaaatcgtttg-gcagATGTCCCTGAAGGTTGTACCATCATAAGAGAACACATACCGATCACAAACCTTTTCACATGTGTATGGTTCAACGAGGTAGATCGGTTTACTTCAAGAGA
| ||| | | | || || | | | | || | | || ||| || | | | | |||| |||||||| |||||||||||| ||||||||||||||||| || || ||||| || || || || |||||||||| || || ||||| || ||||| || ||
gtaggaacaacagacgaacagttttcatatattcatgcctgcatatgtaaaatggattatgtgtggagatttgtgcctgtgcttgcatataattgctgcctccatcttaaaaatctgaagtattgcttatggctgagtttctgcagATGTTCCTGAAGGTTGTGTTATCATAAGAGAACACATTCCAATTACAAATCTCTTTACTTGCTTATGGTTCAATGAAGTTGATCGCTTCACTTCCAGGGA
upper sequence: AT1G53040.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G35210.1 (Glycine max), 3'ss of exon 7
--------------------------------------------gtaatggttttaaccatatgaggatgataaagttccacaattttcttctgttcaatgatcacaattgaaacatttcaaatcgtttg-gcagATGTCCCTGAAGGTTGTACCATCATAAGAGAACACATACCGATCACAAACCTTTTCACATGTGTATGGTTCAACGAGGTAGATCGGTTTACTTCAAGAGA
| ||| | | | || || | | | | || | | || ||| || | | | | |||| |||||||| |||||||||||| ||||||||||||||||| || || ||||| || || || || |||||||||| || || ||||| || ||||| || ||
gtaggaacagttttcatatattcatgcctgcatatgtaaaatggattatgtgtggagatctgtgcctgtgcttgcatataattgctgcctccatcttaaaaatctgaagtattgcttatggctgagtttctgcagATGTTCCTGAAGGTTGTGTTATCATAAGAGAACACATTCCAATTACAAATCTCTTTACTTGCTTATGGTTCAATGAAGTTGATCGCTTCACTTCCAGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacaattttcttctgttcaatgatcacaattgaaacatttcaaatcgtttggcagATGTCCCTGAAGGTTGTACCATCATAAGAGAACACATACCGATCACAAACCTTTTCACATGTGTATGGTTCAACGAGGTAGATCGGTTTACTTCAAGAGA
atttcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggttttaaccatatgaggatgataaagttccacaattttcttctgttcaatgatcacaattgaaacatttcaaatcgtttggcagATGTCCCTGAAGGTTGTACCATCATAAGAGAACACATACCGATCACAAACCTTTTCACATGTGTATGGTTCAACGAGGTAGATCGGTTTACTTCAAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA